Yes but if its so black and white they could even choose to void the warranty over different tires or shock absorbers. It cant be so black and white their has to be some give and understanding on both sides of the fence. I think it would be pretty obvious that an aftermarket exhaust system would not be the culprit of a system melt down. Sure there are some circumstances that could cause engine malfunctions, but they would be pretty dang rare and probably never occur.
__________________
2007.5 QC SWB 4x4
6.7CTD, 68RE, Inferno Red, Big Horn