For a starting mage character, there is a maximum cap for spells they can learn.
A PC Mage has a spell they want to cast, but its level is 1 point over their maximum cap. But the PC also has Flawless Magic, and trying to argue that the +1 to spell casting should help them.
I said "no", since the level of Mastery is a casting bonus only, that only applies after you learn/invent the spell.
But then I thought Mastery is a weird little beast, so perhaps I should check the forum consensus.
Yes. The virtue makes it no easier to invent the spell. The mastery doesn’t even exist in the mind of the inventor until after the spell is invented. I would be very surprised if someone argues for ruling in the other direction.
That said, sounds like the player should alter the arts a little and get that one point at CGen that allows them to learn the spell because it sounds like they really want it.
Agreed that Mastery makes it no easier to learn a spell (ignoring Lab Mastery, which I highly doubt will be relevant here).
Arts, Int, Magic Theory Speciality...It's probably possible to tweak something, although they may have to give something else up.
Or you could just let them go a little over the cap if you want to be kind. The justification is "you spent some time learning the spell in a higher Magic Aura than most apprentices have access to". +1 point means Magic Aura 4, which isn't that unlikely.
(But I agree with the other posters that Flawless Magic doesn't apply here. Casting totals and lab totals are different for lots of reasons. Otherwise, I'm going to go to my GM and ask for +2 Lab total for inventing a spell with a very loud voice and big laboratory gestures.)
There is one exception for mastery ability, which is in the cult of mercury only, which is called Lab Mastery, which allows you to add your spell mastery score to you lab total for similar spell. This might be a useful suggestion if, for example, your PC is missing 1 pt towards learning Ball of Abysmal Flame as part of character generation but is willing to put that specialization in Pilum of Fire. Mercurian only, however.
If you allow Similar Spell bonus in CharGen then there is no need to bother with the mastery as any Sim Spell Bonus will alway be at least +1. I don’t think allowing Sim Spell Bonus in CharGen is a great idea though because then you need to get into which spell were learned first and all that. [EDIT, Continued] I also see it as one of those things that will allow experienced to abuse it and be added confusion in CharGen for new players.
I go with the idea that, when you're doing your character creation for the pre-gauntlet phase, you're being taught spells the way an apprentice should be taught spells during an apprenticeship - by reinventing spells your mentor is teaching you in his lab. Which means I'll allow bonuses that would apply in those circumstances. Frankly, no, you're right, I've never had to discuss with a player whether a similar spell bonus applied to learning XYZ. On the other hand, I've applied magical foci's in the past, and if I brought in a character with a dictated background (e.g. your character was the apprentice of magi XYZ at covenant ABC), then I would probably factor in the aura bonus of the covenant and the lab details, if I knew those lab details.
Then allowing non-standard laboratory routines seems a better way to go. Getting a +1 or +2 is pretty simple with those and doesn’t end up needing the order in which you learned spells, whether the spell is similar, and all that jazz.
Or one could just keep it simple, harsh, and fair.
Or one could go through the tedious process of in-game advancement rules through apprenticeship.
Or if one really wants to bend the rules, just bend the rules. Why bother with elaborate justifications. «You got lucky,» will cut it.
If the magus is mine, I'd not allow it. If the magus is just 1 point below the cap for a spell he needs, I'd just rearrange the XPs so he get that extra point because I kind of like fiddling with that stuff.
If the magus were of one of my players, I'd allow it, because after the tedious and long process of creating a magus they wouldn't exactly enjoy having to redo their Art scores.
That's why I always recommend new players to pick their high-level signature spell first, and then build their arts around it.
Yeah, me too, it's a good practice to first check what you want to do and then wrap your Arts around it, but you know, it is the premise of this topic 
I should have mentioned, the character creation was long enough ago that it is too late to change things.
It was reading something recently on the forums made me wonder if I made the correct ruling.
The various suggestions are interesting, and I will keep them in mind for the next time,