I can't address any HOM if I don't have a map name at bear minimum
The white squares were intended for providing info on the bosses. the info scripts were never written and at this point, never will be. The bosses are going to get removed from the hub map.
Errors? I'll have to take a look at all GFZ2 variants. (EDIT: Could not find error, can you please provide a screen shot or devmode coordinates?)
The problems with the emblems is unfortunate as I can't add the subtitles to the stats screen. However I'll Consider hiding certain levels from the stats screen. a few don't exactly have proper names anyway.
The museum itself will be getting renovated to a smaller art based one in a future major update.
I hate to say this, but going through 3 acts is best option I can provide right now.
Each special stage comes from each versions respective special stage slot. Egg Satellite , while out of place, is part of the 7th set of special stages (can you believe SRB2 had that many?)
The pseudo slopes are actually already in the process of being replaced.
I could, but what's going to happen is the Museum is going to be renovated in a future update that removes all the boss exhibits
The special Stage challenge was actually intended to be a part of this version originally. this is why you see level headers for other special stages that aren't accessible.
The visual glitch in Emerald Coast is a result of the original layout. it was also in the old Christmas demo too.
the only thing I think I can do to try to fix it is add more sectors, but unless it's the remixed version from the dead Christmas mod, I can't add any new walls.