How much is "slightly"? 1/8 inch or less? That's OK. If more than 1/8 get a thin closet flange extender at HD, Lowe's or plumbing supply store.

Yes, provided you use a slightly thicker wax ring to accommodate the gap. Thicker wax rings can be purchase at most of the box stores. This is a typical problem with building up a damaged sub-floor or having put tile down. Good luck!