This is relevant to me since I'd basically had the identical idea for a game, so apologies for the thread-necromancy.
Here's how I'm seeing it:
The Futura simulations took place over about three years between AF 2 and 5, though initial plans and funding started almost immediately after the Fall. Since the active phase of the project took place quite some time after the Fall, I figure that at this point they would have been aware that Earth wasn't going to be reclaimed any time soon and would instead try to acclimatize the kids to the realities of a post-Fall society. That means most of the population would be on Mars or in space stations - and it would be much easier to simulate an environment the size of a single space station than an entire planet.
The book also states that Futura simulations were running simultaneously on three different stations, with a human staff of about 2000 and AGI staff of about 45 - I figure that forks of those 45 AGIs would be shared on each of the three stations. They might have even forked the scientists and researchers, to reduce the chance of variables - science! and all that.
So I'm imagining the simulated kids live and grown up in what I'm currently calling Futura Station, which in their simulations appears to be either orbiting Luna or Mars. The station would be a fairly typical (though relatively small) cylinder hab. As well as the children and their teachers, it would include enough to educate them on day to day social interactions, which means stuff outside of school life. So, I was thinking that perhaps Cognite employed some infugees to play the role of 'NPCs' for the kids to learn from - storekeepers, fake 'parents', the local preacher, special guests at the school and so on. These infugees might or might not be subject experts for educational purposes, but remember their most important quality is genuine humanity, as contrasted to the AGIs. The AGIs fill the role of 'school teachers' while other important roles for emotional and social development would be filled by infomorphs.
So basically, instead of 'boarding school', I'm seeing it more like Truman Show - a small simulation of a population center with some hard limits on how far you can explore. In this case, the hard vacuum of space and the fact that all the shuttles always seem to be out on missions. However, as the Lost Madness becomes more and more apparent, the AGIs are re-purposed to take on more overall control of the kids' lives and it's certainly possible that the sim would warp and perhaps shrink to discipline them.
(The addition of these infugees and AGIs also pads out the potential roster for async character concepts without having to be quite as 'damaged' as the Lost were, since they were presumably exposed to Watts-McLeod when it was introduced to the simulation too.)