I would go with the long bed. Not only do you avoid interference problems, but the longer wheelbase tows more smoothly. If you do decide on a short bed, a sliding hitch might be a better option than a pin box extension. The extension applies extra torque to the frame of the 5er. Some have been known to crack. Before you do it, check with the manufacturer to see if it will void the warrantee.
The new Ford, Chevy, and Dodge diesel engines are all pretty robust. However, IMO, the Allison transmission in the Chevy is far and away the best of the three. I like the Cummins engine best, but the transmission in the the Dodge is a real weakness.
2011 Silverado 2500HD Duramax, 4x4, crew cab, long bed
Palomino Puma 253-FBS, 27' 5th wheel
1994 19' Class B on Chevy chassis