Thanks fr your last modifications ! Merging took some time, so I didn't test many things yet, but it looks pretty neat !
However there seems to be a problem when a layer has multiple tilesets. This can be seen in your examples scenes : look at ortho map loading on scene start.
The "tropical tiles" layer has a glitch, and the graphics from both tilesets are displayed. Look at the small desert-plant : you can also see the other tileset on this cell with same uv.
Sorry if I'm not clear, it's pretty late here, I'll make a better report tomorrow !