I asked mine again the other day (just as a reminder to him). Again, he said about the only thing that would cause it to not be warrantied is if you did something way out that caused it. The example he gave was cutting into the wiring and it later shorting out and causing a fire, etc. Another example was rejetting to lean and burning a hole in a piston, etc. He said most after market accessories like tires, pipe, etc are ok. I didn't ask about ruining a cv joint due to big tires or being pulled out of a mud hole with the wheels turned and popping them out.
Save your old parts. I don't care what the dealer says, unless he's your dad or something, be prepared to reinstall your old parts when looking for warrenty work.
I have had too many experiences with too many dealers that say one thing and do another when the time comes to pony up!
I don't condone or suggest anything illegal or immoral, I do encourage everybody to be as smart as you can be when dealing with dealers. You can be sure that they will be dotting their I's and crossing their T's when making their decisions regarding the repair of your stuff!