multiple keys via HKDF - whats better, one or two applications of HKDF-extract
Realistically, it probably doesn't matter, if all of your premises are accurate.

If it were me, I'd probably concatenate the inputs, then apply a HKDF to the concatenation to derive two keys -- but honestly, it's unlikely to matter.  This is very unlikely to be the weakest link in your system.  Pick something that's easy to implement and easy to understand, and move on: focus your energy on some other aspect of your system.