Thanks for your work! I'm sorry for the trouble, Chrazini. Now that I look at it, it may even be that the no-collision objects on the grass (plants, revealers) instead of the skeletons on the desert/savannah are the issue, since that grass is changing to foundation terrain.
To be clear, the following terrain ids are eligible to change to foundation (27 or 36 for snow): 0, 3, 7, 8, 9, 12, 29, 30, 31, 32, 34
I've forced a bunch of unsolid objects to spawn underneath the huts, and this does indeed guarantee an out of sync issue. As suggested, putting unsolid object generation before the buildings have fixed this issue. I will now proceed to update all the maps with this fix.
Thanks for your help.