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That being said, if you install something aftermarket, the dealership will do their best to blame the aftermarket part depending on the problem. From a company stand point, is it fair that you add on an intake and subsequently more dirt gets lodged into the engine and now ruins the internals? Should the company be held liable because you lowered the vehicle and your camber/caster/toe adjustments are constantly out of whack?
On the other hand, if you install new rear tail lights or a strut tower bar, there is very little those components can do to ruin the functionality of the vehicle. Also, keep in mind that once you mod the vehicle, you have to accept certain things i.e. lowered ride WILL be a rough drive, more power=less mpg's or durability of engine, etc.
Bottom line...I used to mod all of my vehicles. I accepted the risk of losing the warranty before I installed any part on it. I decided now that unless I want a something specific like a good road racer, I need to buy a vehicle dedicated towards that goal. For now, I enjoy my vehicle just as the manufacture intended me to.