I don't think that there's much differnce in clearance in the wells. I can think of 2 advantages to going wiht the stepside bed-1 you can make one wiht all new parts- no new sides for the fleetside at this time. And 2- there are wider fenders (3") for the stepside, those will accomodate wider tires than stock. They are 'glass if you don't mind going that route.
