This has been a talking point for a while. Check out the forums at
www.dieseltruckresource.com, it's a site dedicated to Dodge diesels. There have been several threads over the past year or so that discuss Dodge's position on aftermarket upgrades. There's even been some discussion about aftermarket air filters voiding the warranty!
On a side note, I have not felt the need to do any performance upgrades. Our 05 3500 dually with the newer engine and the 48RE has been treating us and our Monty fine. Our region has some hilly terrain (but not as bad as out West) and we're able to keep speed towing even on the more severe inclines, even passed a couple of 18-wheelers that couldn't hold their speed.
Fred