backer board mystery
If the bathtub flange is too proud of the studs to allow the backer board to fit acceptably, the studs should be shimmed out so they are even with the flange.  If the manufacturer of the tub says so (and they probably do), the backer board should go over the flange.  Find (or make) some wood strips of suitable thickness, and glue or staple them to the studs above the tub flange.