Spyke, I posted the same question about a month ago.
You are correct, the rear of the bed rail is REAL close (like 1/4 to 1/2") away from the bottom of the camper overhang, while the front is more like 1". The bed appears to have slight tailfins!
I fixed this by installing an additional rubber bed mat (so now I have two). Plenty of clearance at the rear now.
Also, be advised that the fuel door is in the wrong place! If you are using Torklift frame mounted tie downs, the fuel door will only open 3/4 of the way.
Dodge also didn't fix the narrowest tailgate opening in the industry with the 2003, so if your bathroom or gray/black water tanks protrude beyond the 4' wide section, its a very tight fit with the narrow tailgate opening.
One thing they did improve though is the ride with the camper installed. My '03 (3500 SRW) without airbags handles the camper much better than the '01 (2500) with camper package and airbags IMHO, especially the corners. I attribute this to the wider spacing of the spring packs and the overloads actually engage with the camper on the truck (they didn't on the '01).
Hope this helps.