In Maya, however, each layer is a single plane with subdivided sections. Then I UV mapped each subdivision to the same area on my texture atlases. When I imported the whole scene into Unity, I only had 4 game objects to deal with. I am using the Unlit/Transparent for my 4 texture atlases (not the Transparent Cutout...it doesn't deal with transparent edges well). But it seems the significant difference between these two approaches is the number of objects in the scene.
I'm guessing there's not a way within ex2D to "combine" sprite objects?
I hope that all made sense :-\