I agree, this really depends on how focused the player wants his crafter to be. If you have only two or maybe three "craft skill" equivalents you want to do really well (say, blacksmith, weaponcrafter, and possibly armorer; or bowyer and fletcher), then yes, focusing on spell mastery makes sense. But I had the impression that the OP really envisioned a very "general" crafter, capable of making ships, sculptures, weapons, carpets, food, cathedrals, thatched roofs, boots and possibly origami 
If that's the case, one should really ditch spell mastery in favour of "general" finesse, and in fact strongly consider doing a lot of his work spontaneously (stuff up to level 5, and, when the character is older, up to level 10 can be done without fatigue and without risk of botching).
Both of the references about Int+Finesse are specifically for Creo Magic (where you create something from nothing).
Neither of the boxes on Craft Magic (HoH: S, p. 61 or Covenants, p. 49) specify an attribute, meaning it would probably default to the aiming rules ArM5, p. 86), which seems to have been assumed by the author of the Craft Magic rules in covenants. These rules also predate HoH: S by more than a year, so I have to assume these are the original rules(-as-intended) for craft magic.
Thus perception it is, which also has the advantage of not providing yet another use for Intelligence.
Thanks to all your suggestion, Hieronimus Fafnerson (thanks ezzelino !) is starting to shape nicely. I updated the initial message to capture the change he is undergoing.
So I went the way of the Strong Faerie Blood (God) to start with a +2 Sympathy bonus on my magic-crafting (finesse), which could increase further as I gain warping.
So far Finesse roll are at: Int (+3) + Finesse (+5+2) + Sympathy (+2) = 12, just out of apprenticeship, so I believe I am on the right track. Superior quality is achieve at 12 +3 (because of Craft magic), so it is a solid base.
I decided to take Strong Concentration since I want to trade Finesse difficulty for longer spell to maintain. It might be overkill since most of concentration roll I need when building will probably be around 3 (so with Stamina of 1, and concentration of 1 it should be no issue). I need to keep concentration for 30 rounds to replicate a month work, so probably only one Concentration roll (5 minutes).
Still 5 virtues/Flaws to take, so I am pondering Flawless magic, Major focus (manipulating objet) (I realised, I cannot learn the variant of Mystical Carpenter at Conc duration, so the focus will help me), Free Expression, Famous, Cautious with Finesse (I believe it will be a must to take because of the Sympathy I will be using).
I discarded Learning Finesse from mistake as I don't plan to fail 
Other option I am looking at:
Replace Strong Faerie Blood + Faerie Legacy + Cautious with Finesse is worth 5 virtues, to grant a bonus starting at +2, going to +6 (Faerie upbringing) as Twilight set...
With Flawless magic + Mastered Spells cost 4 virtues and is more flexible if it takes some combat spells it will be more efficient (Sympathy need to be link to a subset of a Form, so Craft magic -Terram is one, Craft magic - Herbam another one, hence it won't apply to Crystal Dart or other offensive spells). He will start with two spells (one Terram, one Herbam) at +4 Precise casting and one at +2 (Crystal Dart or Wielding the Invisible sling, multi cast, precise).
Of course, I could squeeze both, but it won't left me with virtues to round out my magus...
Ok, it sounds like this would be a form of copying... I'll have to wrap my head around it.
I was thinking that too.
Okay, yeah, that makes sense. Knew I was jumbling something. My bad.
So because they tell you the specific difficulty to bind a book with different materials creating that book ceases to be craft magic replacing a book binder? I don't buy that at all. Being specific about difficulties shouldn't change what something is, and if it does we have a table of difficulties that would scrap all of craft magic.
A&A also uses Intelligence + Finesse (regardless of Creo vs. Rego) for artwork via craft magic. So the Intelligence parts are not limited to Creo magic.
Again, Covenants lists doing bookbinding via Rego craft magic as using Intelligence. Thus I'm really not sure we can conclude Covenants make any such assumption about Perception even though it does have examples using Perception, too.
Ok. Sometimes when i am on doubt, i say jsut "Finnes" roll.
So does Covenants in many places.
Yes, from there I learned.
Again, I find this statement seriously misleading in its vagueness.
Covenants lists two variants of the same spell to bind a book (in a section that is not the section about craft magic). In both cases, getting a sound binding (what a master bookbinder would achieve with a Craft score of 6) is automatic. No finesse is required to get the sound binding; at the same time you can't create a superior book, or an excellent book. However, if (and only if) you want to add a "special effect" involving incorporation of unusual materials, in both cases you have to roll Int+Finesse matching a given difficulty.
At the same time Covenant explicitly gives, in the section about craft magic, several examples of spells that really are the essence of craftmagic. E.g. a spell that allows you to work wood as a carpenter; one that allows you to work iron as a blacksmith; one that allows you shape glass as a glassblower would.
In all these cases, we read sentences such as: "The magus must succeed in a Perception + Finesse roll substituting for the smith’s Craft: Blacksmith roll, with +3 to any Ease Factor" that very clearly say that you are substituting a Finesse roll for the appropriate Craft skill roll whatever you may want to achieve, and remind you of the extra difficulty of doing it through Finesse.
That said, I do agree that serious confusion seems to have crept into the line about whether Int or Per is the appropriate characteristic for Craft Magic. Personally, they both make sense, and I like Per slightly better given how crucial Int already is for magi. This is definitely stuff for errata. Anyone willing to write to David Chart about it?
If Finesse roll for Craft magic is paired with Perception, would Keen Vision apply to those rolls ?
p44: You can see farther and more clearly than most. You get +3 bonus to all rolls involving sight, not including attacks with missile weapon.
It is not a strech to say that it won't apply to Finesse roll for aiming spell. Projecting something through magic with the intent to cause harm fits all the bill of "attack" and "missile weapon". However Craft magic is definitely not an attack.
The only reason the bonus should not apply would only be for game balance/abuse, as a lowly minor virtue would grant a +3 bonus. On the other hand, it can be argue it is a narrow application. I have not strong opinion and would be fine with either way.
More research and readings allowed me to identify three possible profiles, each with interesting background.
They all belongs to House Ex-Miscellanea (I had to strech to get some extra virtues, so there is a bit of optimisation).
All variants have Puissant & Affinity with Finesse as those are core virtues to achieve high Finesse roll. Some are short of a few flaws and all can easily be customised by removing some sub-optimal virtues/flaws that I put to suit the background story and can be made to fit many Houses.
Thanks to all your feedbacks, I was able to select the right books to extract the information I needed. It was a interesting exercise since it was the first magus I was fully building since a long time, and I needed no less than 8 books to gather all the applicable bits of rulings, spells and virtues: HoH: MC, Cov, RoP:F, HoH:S, C&G, A&A, HP and the core book !
First, the Faerie Builder. His sire has some big plans for him in the future, and he needs a pawn with amazing building capacity.
Strong Faerie God Blood - Fafner(+3), Faerie Legacy(+1), Cautious with Finesse(+1), Faerie Heritage(-3), Faerie Upbringing(-1): all in all, this package give character a strong background and access from the start to Sympathy (buildings) at +4 (starting at +2, with 35 xp to bring it at +4), with potential to relatively easy reach +6 (only Warping of 2 will be required).
It is rounded with Improved characteristic (+1), Skills Parens (+1) (it is a bit cheesy, but I needed the extra XP from the start), Affinity with Rego (+1), Independent Study (+1) and Spell improvisation (+1). Finally Free Expression to achieve truely marvellous architectural building.
Additional flaws are: Unnatural Magic (-3) and Waster of Vis (-3), both emphasizing his inhability to use Creo Magic. Finally Warped magic (-1) and Generous (-1) (granting freely nice house to friendly person, which of course will bring troubles - either from Quasitores (meddling with mundanes) or as a tool for his Sire to drag him into his plot). His Faerie Upbringing and Generous traits makes him oblivious of the trouble he can be by just building a nice farm for a friendly peasant who gave me a roof to sleep and some nice warm milk and bread in the morning.
With a Finesse of 5+2, Sympathy of 4, he will start with a nice 14+dice on his Finesse roll for building (+17 if creating some artistic marvel). He still has a +10 Finesse for any other roll. Not as impressive, but still very good.
He might becomes quite popular amongst Jerbiton looking for unique home or signature lab.
Then, there is the Faerie Inspired journeymen.
The core of this character is made of: Major Sympathy (building) (+3), Cautious with Finesse (+1), Flexible Formulaic Magic (+3), Weak spontaneous magic (-3), Homonculus wizard (-3), Deficient Technique (Perdo) (-3).
He draws his inspiration and skills from his homonculus. Since it grants him also the Gentle Gift, he is enjoying working for a season or two on cathedral construction site.
Because he does most of his work at night, there is n the nearby villages the beginning of a legend regarding a friendly and crafty gnome fixing damaged roofs and barns after bad hailstorms (it gives him practice).
To round him. he has Puissant Concentration (+1), Improved Characteristic x2 (to have Com, Pre and Dex at +1 on top of Int at +3), Adept Laboratory student (+1; he prefers to study in the privacy of his lab) and Deficient technique (Perdo) (-3), Nocturnal (-1; to allow his homonculus to walk outside) and Warped magic (-1).
He is starting his Finesse roll at +13, but his Flexible Formulaic Magic allow him to tackle almost any task with a limited set of spells: for quick and dirty work he will be using the Mom duration, but for finer work, he will bump the duration to Conc, allowing him a much tighter control.
Finally, the Hermetic Craftsman.
His core package is: Flawless Magic (+3), Flexible Formulaic Magic (+3), Improved Characteristic (+1), Great Characteristic (+1), Puissant Artes Liberales (+1), Weak spontaneous Magic (-3), Chaotic Magic (-3).
With that, we have a methodic caster, who frowns on any spontaneous magic, considering it as unpredictable and unfit for good quality craftmanship.
He is the kind of dedicated craftsman who will have an holistic view of his crafts: he will study in the future Philosophae and Artes Liberales as well as any Craft who could assist him in improving his work quality.
Hence he is rounded by Apt student (+1) and Independent study (+1) and Driven: becoming a famous master craftsman (-1), showing his dedication to his trade. Finally, he is sacrificing symbolically his hair to the great Architect (Restriction: must be bald; -3).
He will start his Finesse score at 13, thanks to a characteristic at 4, mastery (Precise casting) of 1, and usually a ligature giving him a bonus of +1.
However, this Finesse is not restricted to buildings, but apply to any finesse roll, making him in the long run a master of many crafts.
His first years after apprenticeship will very likely be spent trading his skills for training with good masters in Craft: Architeture, but also Philosophae (to have some Formulae that he could mass produce with simple Craft spell) and Artes Liberales (to be able to make +2 ligatures). Ideally, he would like to achieve 5 in a couple of Craft skill to have a +3 familiarity bonus on his Finesse roll.
This profile could easily be customised to become a Tremere combat engineer in charge of instant fortifications since all his virtues/flaws goes into the dedication expected by such House.
Now I see where you're coming from. I still disagree because it doesn't actually say that. I can see reading it that way, but it really doesn't say no Finesse roll is needed. What if there were a line in The Phantom Blacksmith that read "This spell allows the covenant to make Superior Tools"? Would that then change the meaning of the rest of the spell so you don't need a Finesse roll? Or is it just pointing out what can be accomplished toward the purpose of decreasing mundane workers?
For example, high school geometry allows you to derive the formula for centripetal acceleration. Does that statement imply that everyone who can do high school geometry can derive the formula for centripetal acceleration from it? Rather, it means all those who can do high school geometry have the tools to do so if it is applied properly. "Allow" is not the same as "guarantee."
In the cases of the bookbinding spells, I would require a 9 to bind the book well enough for the Sound Binding bonus. But I have no idea how much harder it might be to do the crafting if a magus incorporates some different materials. Fortunately, the spells tell me how much more difficult it gets.
That same section also uses Communication + Finesse and Dexterity + Finesse when using an enchanted item to cast the spell, explicitly to substitute the Finesse roll for the appropriate Craft skill roll. ArM5 says the user makes the targeting rolls for the device, which is consistent with the user making the Finesse roll for the device here, but there are no statements that making the roll for the device should change the Characteristic. So even that section does not seem to consider it always Perception.
Between Perception being used in some spells, Communication or Dexterity being used with an invested effect, Intelligence being used in some spells, and Intelligence being used for artwork via craft magic, I find it extremely difficult to conclude the intention was to use Perception. This is why I haven't argued for a different specific Characteristic, either. I've only argued against such a conclusion. I believe that logically drawing such a conclusion that any one Characteristic was intended for Rego craft magic is impossible.
I think it was left vague for a reason, but that lack of clarity has led later writing to make it even more unclear when different Characteristics would be used. My problem is not that there is not one Characteristic to be used. My problem is that I cannot find the pattern off of which the example selections of Characteristics seem to be made.
I'd be dubious about using a longer duration to make craft magic easier - page 49 of Covenants says "Extending the duration of a Rego craft spell makes the spell perform the same actions over and over again on the same starting materials - it is almost always inappropriate". I think you could certainly use standard Rego magics with concentration duration to move objects about to construct things, but that this would require knowledge of the appropriate craft skill to a an equivalent level to making the object mundanely (possibly as well as finesse to acheive the required delicacy in placement), so that you knew where abouts to move them to.
I see your point now, but I still disagree. The "bookbinding" spells simply state that they produce a specific effect. I assume that the effect is automatic, since the spell doesn't say otherwise - whereas in the "blacksmithing" and "carpentry" spells the need for a Finesse roll is made explicit.
Agreed. I wouldn't mind multiple characteristics either, but neither the RAW nor the examples give you a (consistent) hint about how one should go about it. Errata is needed!
You realize that Faerie Legacy does nothing more than give you 10 xp?
Agreed, Faerie Legacy is about the least useful if not the least useful Minor Virtue in the game.
Keep in mind you can only have one Hermetic Major Virtue (at character generation), even in Ex Misc (the free major is supposed to be non-hermetic).
Mmmh... true. At my first reading, I understood that I needed the Faerie Legacy to simply have the Sympathy trait, but after re-reading it, it is clear that 1) it is not mandatory and 2) I don't even need Strong Faerie Blood. Sure, it makes the background a bit weaker, but I am getting back 3 Virtues points...
I could take this Flawless Magic that I like so much (probably more than it is worth ) and it will immediately compensated the one point Sympathy I am loosing. The advantage of that is that the Faerie Builder won't be limited to only building, he will still be quite skilled in other crafts.
I knew it ! I was under this impression, but I could not find it re-reading the core book. Now I finally found it in the side bar p37...
Two options: 1) Poor puppy dog look at my GM (might succeed on a critical roll of 36+ ) 2) Back to the drawing board - it is not a big deal, the FFM was their to maximise the mastery application, but I understand that outside of my specific application, there is definitely room for brokeness.