I just got back from my dealer. I was looking at some asseccories in a catalogue. I asked the service manager about an intake and dpf back exhaust. He said as long as you don't drill any new holes or mess with anything electrical it wouldn't void any warranty.
I jokingly asked him to put that in writing. To witch he responded very seriously. "Absolutely, I will and, I have".
So I guess it wouldn't be a bad idea to go talk to the service manager where you would have any warranty work done and ask him. Maybe find out if he'd be willing to autograph a statement for you. That way you KNOW your covered.
This might seem a little extreme but we are talking about very expensive systems in this truck. I'd rather seem overly cautious then left holding the repair bill.