I would not raise the fee issue at ABQ. If you are asked to pay, DL may correctly collect the fee for its domestic ticket. A decent chance that the check-in agent does not. The interline agreement has nothing to do with either the fee or DL's policy regarding separate tickets, e.g. yes to ST and no to others (even where it has an interline agreement).

Larger issue is that AF is unmerciful on rebooking if there are separate tickets and you no show. Give yourself 2-3x the MCT.