Just spitballing, but the laboratory Structure Virtues "Auspicious Shape" and "Well Insulated" logically should be free instead of minor if you did custom building construction to include them from the start, right?
I mean, yes, if you have to retrofit an existing room in an existing building to add them, they'll obviously reduce usable space in that room compared to if you didn't retrofit the room. But if you have a freestanding, physically-pentagonal building, with walls that were highly insulating from the start, well, the relevant Space for your laboratory should be the space inside those pentagonal, well-insulated walls. That you're taking up "extra" land outside the laboratory should be irrelevant, and thus Auspicious Shape and Well Insulated shouldn't count against the Virtues you can fit inside your laboratory.
There are a couple such virtues that need to be rethought. Gallery, for example, may make sense to take room in a place where you have to add staircases and support pillars, but it could be thought from the start. Worst - feature: high ceiling. How you add that to an existing lab that is in a building, and why it takes size... I suppose it makes sense to take size if you already have a multi level lab and you're demolishing a floor or two to make that room. And then there are virtues you pretty much need to find and build a lab arround - Regios and Portals, for example.
But yes, many of our home brewed spells to conjure building are made with the thought of having such free virtues that are shown as costing size, here and there.
I thought that Auspicious Shape used some of the Size for the arrangement. For example, nice, right-angle furniture just won't fit well in the corners of a pentagonal room. This is more of an issue for smaller spaces and for some shapes than others. But a simple baseline of losing a useful point of Size seems reasonable. Now, I'd let you just start with them automatically if that's how the lab is built, but I'd stick with the book's Minor Virtue's use of space.
For those walls, I think you're essentially comparing apples and oranges. If you measure the lab space as the full space minus thin walls, then with thick walls you have lost some of that space. But if you measure from the inside of the thick walls, then you've already accounted for that lost use of space. So if you recalculate the Size of the lab based on thin walls rather than inside the thick walls, everything should be consistent. Again, I'd let you have it automatically if the lab was built this way.
This crossed my mind, but the specific examples given aren't consistent with it. The example Auspicious Shapes are pentagon and hexagon, while the example "doesn't count" shapes are square and circle. The geometric trouble is that a (regular) pentagon or hexagon is midway between a square and a circle on pretty much any attribute. An explanation as to why a hexagon is inconveniently shaped (and thus wastes space) compared to a square would in every case I can think of apply just as much to a circle, and similarly any explanation as to why a hexagon is more inconvenient than a circle would seem to apply to a square.
(And in the matter of the shape being awkward, we then have the literal Awkward Shape Flaw somehow giving people more effective Space for installing Virtues, instead of reducing the useful space implied by the square footage. These shape Virtues/Flaws are balanced in gamist "pay for bonuses, get paid for maluses" terms, but the physical logic doesn't convince me.)
It wouldn't matter, except that the difference between "Size 0, and the insulating walls are outside the lab, defining it" and "Size +1, and the insulating walls take up the space for a Virtue" is that the latter is a Safety penalty.
So, yeah. Both being minor Virtues instead of free make plenty of sense to me if you assume that that magus is starting with space in a building and then retrofits 'em to it, so he has some sort of internal walls or whatnot added in what could have been useful lab space for Auspicious Shape, and the "extra partition wall or a layer of thick curtains" in the example for Well Insulated.
We decided to embrace that.
Our saga's well-funded covenant was constructed as a covenant, and we have big, well-stocked labs for free - not counting story problems concerning upkeep and why our covenant was created*. We don't track space. Any further improvements** are simply bought by Refinement or taking Flaws.
*So far: Pirates, the Bishop hates us, zombie rat swarm, the Black Wolf, the destruction of a several buildings and two labs, a grab bag of curses, and one dead mage. (But it was a Tremere, so ... meh.)
**So far: Cold forging smithing equipment, a breeze, and a bad bubble bound in a brisk-bowling bronze ball.
I see where you're coming from with the circle and square v. the pentagon and hexagon. That is strange.
Your comparison with the Awkward Shape Flaw, however, is off. You can set up shapes that have the same square footage but, by virtue of walls, blocking views (likely causing problems with safety and aesthetics) while giving a lot more space to hang things or attach things than a big, empty room.
Those do, however, leave out the Really Poorly Designed Space non-existent free Flaw that gives you a Size penalty. By this I mean things like the hallway like room that needs so much of its square footage to move about that you effectively have less space.
Yes, but I'll accept that as it just being really hard to simulate everything perfectly. At some point we just have to accept that we'd need many, many times as many rules to be more realistic or we can accept things will be more off when we cut down on rules.
But you can always house-rule things. Consider magic items. You get the benefits of a Virtue without the space. There's no reason a troupe couldn't decide this can be done non-magically with certain Virtues.
Highly customized construction from scratch should have some additional cost, although that may be a more ordinary mundane cost rather than a virtue cost.
Right, my use of "free" was specifically in the same sense that Dedicated Building, Defenses, Grand Entrance, and Superior Construction are all "free" Structure Virtues (Covenants 114), even though they obviously require resources to implement.
The book only says that square and circle don't count as auspicious. I take that to mean that these shapes are too common to be auspicious, without saying anything about the use of space.
That a round room does not waste space, because it does not cost a virtue is an artifact of game mechanics. It comes down to what callen said about a compromise between simplicity and realism.
I will point out that a pentagram is not a pentagon. A pentagram is a five pointed star shape, I can easily see how there would be wasted space.
At some level part of the question has to be what is meant by space when you are designing the lab. If it is the cost of building the walls the it certainly makes sense that extra thick walls or a star formation would use more "space". If it the amount of stuff that will fit into the room then again awkward shapes would mean less useful space, but insulation, unless you are talking large wall gaps, does not.
(That's the sort of thing I meant when I asked if I was missing something. Reading "hexagon and penta-" my brain just autocompleted it as 'pentagon' instead of noticing the book actually finished with "gram" on the next line.)
Of course, that just heightens the contradiction with the immediately-prior "hexagon" example in Covenants, but that's probably an erratum. Assuming it was actually supposed to be 'hexagram', the traditional shape of the Seal of Solomon, it makes perfect sense for Auspicious Shape to be a minor Virtue instead of a free (that is, non-space-costing) one.