Just a note, for a world with some caverns you could always use 2-4 separate interiors aligned together. Although I think that spawns lighting issues, I'm not sure.
Anyway, I look forward to this. Try to reference the textures from their locations in the base files rather than repackaging them, though, I use a subtly altered stud texture and I know some other people use their own edits. The difference is pretty jarring when you look at them side by side, and if you're trying to cut down on download times it's a few less files - albeit small ones - that don't need to be downloaded.
As for skybox ideas, the semitransparent one seems like a good idea. The whole atmosphere could be a semitransparent cube about an 8x cube out from the ground interiors.