Remember that part of the culture of the Roman Tribunal - at least for this game- is keeping things quiet: the Dominion is Strong in the Roman Tribunal and angry commoners is bad for everyone. As such the Magical Fortress will probably not work. A mundane castle constructed through magical means is possible, so construction time is probably not an issue so much as willingness of magi to dedicate time and Vis into constructing fortifications versus spending silver and letting mundanes handle it more slowly. I could easily see conjuring a mystic tower the first year to establish a presence and then building up from there with more mundane resources...
Of course PeTe doesn't take vis, so an underground section, especially one built early on, also makes a great deal of sense.
I was thinking above ground, just with an extensive basement. That way the place might seem just a meager yet solid stronghold from above while housing enormous amounts of stuff below.
So are we looking at Tower keep with artillery?
Next question- income source(es)- obvious possibilities are some form of herding or fishing. If you wish to take the road hook then some form of trade based income would make sense as well (though this might also necessitate an outbuildings hook, or justify labyrinthine as you have rushed to keep up with commerce). At the same time we should consider at vis income the covenant will have established.
I'm currently writing my parens magi as a terram specialist with "Conjuring the mystic castle" as something they could just learn straight out of gauntlet, so a tower keep is very possible.
If we want to have better wizard's labs (coughs teaching specialisation coughs) when play starts, do we take it out of the seasons of development for the elder magi, or do we pay for it out of build points using the rules from Covenants? I can spare a few seasons to refine the size down and add features, but I'd like to know if we can do this or whether to wait until we start in 1100.
I'm going to allow either- though obviously some virtues can only be taken in the building- however where a single condition is described by a combination of virtues and flaws you will only need to pay for the net cost- also refinement cannot be bought with points...
so for example a feature-focus combination may be taken for free, if it is part of the design of the lab (say an alter from the temple that was already in the middle of the lab), or auspicious shape combined with awkward shape... or perhaps a lab which is still outside with natural environment and outdoors...
The build point system is a little bit screwy. Mostly it's OK. The thing that is totally off is buying labs. What can be built by a non-magus with a not-super-high score in Magic Theory over just a few seasons costs the BP equivalent of hundreds of pawns of vis. It's much better to put some points into a specialist or similar. Plus then you can design as you go a little better.
Would this be one magnitude higher to make it 10x the volume? 
No, because using guidelines of best arts of 10, and using puissant Creo and puissant Terram with no magical focus, you get Cr 13 + Te 13 + Int 2 + Magic theory 4 (terram specialisation) + aura 3 = 35, so the base version is just learnable for a character without a magical focus. The parens has got Life-linked Spontaneous magic so is a bit more of a generalist, so I didn't give them a focus so as to encourage a little more diversity among the magi. It does mean if my apprentice wants a focus, he'll have to find a mystery cult to quest for it from - but I think this adds to the fun.
The character does have the arts to start doing tunnelling/trenching spells if we want to dig out a covenant or build defensive earthworks.
Point taken about labs - the parens will have enough teaching to do the basics, a few seasons of refinement and adding lab improvements can be done while the apprentice mops the floor or studies books.
keep in mind that you don't have to start apprenticeships in 1100- that is simply the earliest time it can be done. So if you spend a few years refining your labs and specializing in teaching or other areas that is fine...
That's not a limit. That's a suggestion about poorly designing characters, which itself is a suggestion based on poor analysis and is not really valid.
Lets take a moment here to look at this- the covenant has been a chapterhouse for 50 years. It is entirely possible that during that time a magus no longer with the covenant cast conjuring the mystic tower or a variation on it. If it was one of the parens magi they would not have to be right out of their gauntlet when they did so. We can simply stipulate that there is a tower keep and that the spell was a part of it.
As to the point cost of labs, keep in mind that a lab is a combination of a building, equipment, and time of a magus, plus being fairly central to a magus' life. Also I do not assume that the build points are balanced in terms of the way they can be used. 5 vis is not equivalent to 10 pounds of silver. Its simply a matter of what you are willing to pay to start the game with versus looking to get it in play.
Hell, there's nothing stopping us from saying we contacted a magus from another covenant, and had them summon up a mystic tower or the like. I always got the feeling that the Hermetic community was relatively tight-knit: even if you don't know everyone personally, you'll have heard (by reputation) of a great many members of the order. Stuff like a new covenant being interested in some fortifications against the odd heathen invasion just seems like something should just...happen, from time to time.
You could get little 'help wanted' ads with your regular red-cap dispatches!
Certainly getting a tower conjured at the start 50 years ago can simply be written as fait accompli with the boon of a tower castle.
Seems reasonable to me.
Do you have artillery and what source(s) of income would have been developed? Both silver and vis...
Yes, which makes things much easier.
I still suggest a very large basement. It could even be an enormous foundation stone that gets carved out as needed to make room for new labs and the like. The nice thing about that is you can customize the appearance (size, shape, style, etc.) of your lab and living quarters even more than otherwise.
There doesn't seem to be a virtue or flaw that matches this- I'm going to simply assume that PeTe is fairly simple and accept it as finished... unless you want the under- the covenant basement to also be a mine of some sort that produces revenue...
Right now we still need to define income and most of the stores regarding money and vis, we also should add any "incidental" flaws or virtues (for example, suffrage or gender imballance0 that could be a result of magus principles or simply quirks of development (as a defensive outpost it may well have had more men, for example)
I'll throw out an idea for a vis source: Ghosts! With the presence power they can produce vis. They just sit around and vis shows up. That would also give us the haunted hook. Possibly the temples could be haunted.
For income if we're by the sea that makes the most sense in my opinion. Probably something like trade or salt production.
Any Rego experts? Salt production (and plenty of fresh water along with it) is pretty trivial. Make a lesser enchanted device and have servants do it.
With the vis source will come a rival flaw for whomever was harvesting it before you showed up- this can be either the minor or major version depending on the strength of the covenant that would be upset over you claiming what had been their vis source prior to your arrival 50 years ago.