Interesting thoughts !
Size:
We know that in the Second Age, there were 30.000 scrolls to be distributed meaning we can assume there were about that amount of undertowners who migrated toward the Free Glades. There surely were some who remained or died, but in the end, that number gives us a good estimate of how big undertown was.
I always understood Sanctaphrax to be more like a big university, just like unis today often have thousands of employees and their own cafeterias, shops, dormitories, democratic system and even postal service.
But calculating the size of the pot is a really good idea,even if CR probably just painted something.
Sky-scholarship useless
I guess you are sort of right about sky scholarship, it often seems like a bit of a waste. But then, all of the Edge's science is a bit unscientific. They just assume something and then don't even do experiments or anything, but just assume that the great rock will be healed by lightning just because, and a solution for the growing rock will be found in the Deepwoods, although nobody knows why and when and where to start the research.
But that could also be because power corrupted the scientific research, and at some point authority like Hax Vostillix counted more than an amount of sourmist particles that seems slightly off (as Quint notes in TWK) and Stormphrax is considered holy, making it no longer really an object of study but something higher and somewhat untouchable.
Potion:
The potion school being a reminiscent of earth-scholar time is a good idea. It might be, just like DDB said, that it was tolerated because they needed someone to help them assassinated the victims of their intrigues and taken over by sky-scholars.
School of paint:
Could it be that the school of paint was more responsible for making colours and creating new styles that other painters just followed?
We mostly know of portraits of academes and such, so I guess you are right about it being all commissioned and not free and creative. The Knights Academy and the Palace of Shadows mostly have mosaics, statues and wooden carvings, that could'be been the Renaissance of the Edge.
Sky-Scholarship :
The interesting thing about how positive or negative sky and earthscholarship are to the reader is that in The Immortals and the early Cade Saga, sky-scholarship seems to be pretty good and useful, inventing new mechanisms to get more stormphrax and using it until again someone bad, in this case, Quove Lentis takes over.