Isn't that the mesh used for the vanilla night sky? Unless you plan on using entirely different textures I don't see why you'd need it. It's not really part of the weather, anyway.
Yes, but Arthmoor might have done something to it that requires us to have an altered copy. Perhaps for Real Lights skydomes in caves or something?
I'll take a look at it in NifSkope and see if I can spot any differences.
EDIT: I have 3 stars.nif files: one vanilla BSA, one vanilla PYFFIed, and the one in All Natural. The AN one is closest to PYFFIed in size, with size being 50 bytes larger. As for difference in NifSkope, 14 NiTriStripsData Num Triangles has a value of 513 in AN rather than 510 in PYFFIed, though that's probably PYFFI getting better since it was run on the AN mesh.
That's the only difference, so I think we can remove the stars.nif in AN.
EDIT 2: Just fixed another bug in the SI script that could be the cause for instant transitions, and a few others that could also cause problems.