Working on a patch to fix all the reported bugs since some of them are quite serious! I may come to regret this with how unstable the project is but It's worth trying.
Unfortunately, short of preventing saving in these situations there's not much I can do to fix this issue as the scene changing is necessary to prevent another... rather worse issue where you can get stuck 'outside' of the map due to the under-over tile calculations bugging up. (The engine wasn't made with overhead tiles/depth maps as a default feature) Not being able to save in certain scenes is preferable to soft-locking you if you do. Do you know of any other scenes this happens in other than the one in the Gaia scene?