having said that, if you cause the damage, they won't warranty it... but the simple act of changing to another vendors parts alone cannot be stated as a reason for refusing to service under warranty... obviously, if you were to no tighten the headers on and cause the engine to overheat, it wouldn't be covered... or anything like that
For me i experienced an issue with my front brakes locking up. I switched out my levers, so when i went to ask if my warranty would cover it. They said since i swapped out my levers, they would not. Apparently it voids the warranty. I am guessing if you change something to an aftermarket part and whatever goes wrong can be linked to it, they will probably give you a hard time or not cover it if it goes wrong. I mean i like mods, so i am not sure why i got the warranty.