Basically, I think that as more faces are made and released, that the current system of combined eyes + mouth could get very bulky and messy.
For instance, take the Doe Eyes. There are 10 items for Doe Eyes. 5 with open mouth, 5 with closed mouth.
If the eyes and mouth were separate layers, this number in the shop could be reduced to 7.
5 Doe Eye Colors, and 2 mouths, Open Mouth and Closed Mouth.
Perhaps not much of a reduction, but as more and more items are added...
Plus, then we could also mix and match other faces... For instance, Blush Fire and Smirking Mouth.