Do you know if the Mastercraft bench seat folds down? If it folds below the height of the tub sides...you should be good to go.
You could always ask Badger if he could make a custom cover, something that would 'pocket' the back rest...similar to how the full tonneau covers the head rests on the front seats.
"It insists upon itself" Family Guy
"Your Defender insists upon itself" Dave Parker