I'm not really qualified to go into this, but maybe read a little bit about the Pauli-Exclusion Principle works. I get the feeling that might be illuminating.
> > Atoms are able to select which indistinguishable electrons will fill the lowest energy orbitals.
> Or might this imply that the electrons are actually distinguishable in some way? Or maybe I should re-phrase; could each electron actually have some (possibly hidden) identity?
I still don't see what that has to do with the above. The context with and relation to their surroundings seems entirely sufficient to distinguish between electrons, so they're not indistinguishable, even if, in isolation, they are.