While I was getting our oil changed I asked them about aftermarket parts and warranty. This is what I was told, which is common sense.
What was said is no matter the aftermarket part it will not void the drive train warranty (unless huge, Nitrous, turbo, SC....)

I asked about the intake, no problems as long as some sort of water protection is used to stop hydrolocking.

I asked about the header and told him that it would delete the cat. He said its not a problem. The header shouldnt cause engine problems anyway.

So basically, you shouldnt have problems with warranty work if minor bolts ons are added. Keep in mind all dealers are different.