Just an idea:
In the same way that multiple tilemap, layers are handled by generating multiple subscenes in godot, perhaps a single tilemap layer that has multiple tilesets could also be split out into subscenes? Each layer could be a Node that has each set used as a tilemap, or maybe only tilemaps that have multiple tilesets used would generate a child tilemap parented to the layers base tilemap.
Just an idea: In the same way that multiple tilemap, layers are handled by generating multiple subscenes in godot, perhaps a single tilemap layer that has multiple tilesets could also be split out into subscenes? Each layer could be a Node that has each set used as a tilemap, or maybe only tilemaps that have multiple tilesets used would generate a child tilemap parented to the layers base tilemap.