That's exactly the set-up I have, F250 6'-8" bed (short bed) with the 4-section BakFlip cover. For towing I fold the cover to lay flat, not against the back glass of the cab. There's even bungee-cord eyelets to secure the Bakflip, and I have no clearance issues with turning the fiver. I currently maintain 7" of rail clearance, and no issues with the BakFlip folded up on itself. It's a great cover - when unhooked, I just close it up and the hitch stays out of the elements.
2016 Salem Hemisphere 368 RLBH / 2014 F250 Platinum 6.7 Powerstroke / 2011 Bayliner 315 / T/5.0 MPI