Standard service bodies have bed rails that are at least as tall as the stock bed and generally taller. So you can expect greater clearance problems. Also, the side boxes narrow the bed width to around 50 inches while most common extended pin boxes are longer than 25 inches, which means the back of the pin box will hit the side of the bed. Finally, the cross members are taller than a stock pickup bed, making the bed floor higher so a normal fifth wheel hitch will sit too tall. There are shorter hitches designed for flatbeds, but they can have the opposite problem of being too short for a service body. For these reasons, most RV hauler beds are really glorified flatbeds.
My ordered my service body 11 years ago from RKI in Houston and for a $200 engineering charge, they modified the stock height to my request. With the reduced height and higher load floor, bed depth is just 12 inches, but it still works for carrying things. Overall bed rail height is 50 inches compared to 55+ inches for just about all pickups today. This reduced height results in 10 inch bed rail clearance but more importantly allows the back of the pin box to also clear the rails. The lower height also means I don't need a step stool to operate the hitch. Weight increase compared to the stock bed was only 400 lbs. This year I moved the service body from an '03 2500HD to a '13 3500 SRW.
Today I doubt that RKI or anyone else would do a custom service body for just a $200 up charge. So, if I were starting from scratch today, I would probably buy the lowest height stock body available and then use a Sidewinder pin box to avoid contact with the bed rails.