As far as I can tell, it’s because my shirts are separate meshes (to allow for overlap of armor). Vanilla shirts retexture the character’s skin. Since my shirts don’t have that texture information, the character’s skin is presented as “void/empty.”

At least that’s what I think it might be.

Actually quite pleased to announce that I may have found a fix for the blackened skin bug. If all goes well it'll be a part of my next update along with a round of fresh screen shots for everything.