I drove four 04. 5s at the product introduction last month. None had the hesitation, vibration, or drone under any driving conditions I used. I know this is not a consolation to those with a problem, but it suggests that the condition is not inevitable or normal. My 2004 (305 hp 6 speed) has none of these problems either. I now have DD 4" exhaust on it, but I drove and towed with the stock exhaust and it was OK as I recall.
If your main interest is solving the problem, even if it costs a bit, once you have documented it, talk to the service manager and tell him/her you are going to put on an aftermarket muffler at your own expense to see if that helps. Get his concurrence that he will not later blame your muffler for a pre-existing problem. Another muffler just might fix it--I don't know. I do know the stock muffler is a heavy beast with 4 (if I recall) crossways baffles in it. I'd rather have a straight through muffler with perforated core, either Magnaflow or Walker 21471 anyway. The 04. 5 already has full 4" exhaust so you don't need to buy everything.
As for the hesitation, I don't know. I have never experienced it so I don't know if it could be low rpm turbo lag or what.
I know not everyone agrees (since warranty should cover everything defective), but my approach is to fix something, and if Dodge can't or won't figure it out, I'll do it myself because the truck overall is the best out there. Sometimes we TDR members, and aftermarket vendors, are the best at figuring out things. That goes for the killer dowel pin, exhaust manifold woes, etc.