That would’ve annoyed me too.
If it fits in the sizer including wheels, that should be the end of the discussion. Southwest’s policy is based on the sizer. Saying “it fits but you still have to check it” makes no sense unless they were planning to start gate checking a bunch of bags for space.
Sometimes at BOS they preemptively gate check rollers if the flight is full, but in that case they usually just announce it and ask for volunteers. Pulling you out of the seating area and insisting even after it fit is odd.
The part that always stings is seeing bigger bags get on with no issue right after.
You did the right thing filing a complaint. At minimum you might get a gesture credit. I wouldn’t expect a huge outcome, but it creates a record.
Out of curiosity, was this an early boarding group or later? Sometimes they get more aggressive once bins start filling up.