As with many things, the answer is...it depends.
The Magnuson-Moss Warranty Act says that a manufacturer cannot deny a warranty claim because of an aftermarket part, unless the part in question actually CAUSED the problem that the warranty claim is about.
That means that if you install aftermarket shocks, and then your turbo blows, the manufacturer cannot deny you warranty coverage on the turbo. (Unless the shocks somehow directly caused the turbo failure, which defies reason.)
But if you install an ECU chip upgrade that increases turbo boost, and then your turbo fails, the manufacturer could probably deny your claim. It is reasonable to think that increased boost could lead to a turbo failure. (That doesn't mean it does...we have not seen a single turbo failure attributed to an ECU mod.)
Of course, that's just the law. Reality is that the dealer can make life awfully hard on you if you pull in with your lowered car and they decide they're not going to cover your turbo failure just on principle. While the law is on your side, the dealer service department may or may not be. For that reason, we suggest you get to know your local service manager. Be honest with him or her; ask what is the department's policy on aftermarket modifications and warranty service. You'll find a range of stances, from super-conservative ("We don't work on modded cars, ever") to liberal ("Yeah, we even install turbo upgrades here at the dealer!"). Find a service department you can live with.
Note that we do NOT endorse any kind of deception in terms of warranty coverage, including parts-swapping or any other "mod reversal" to try to gain warranty coverage. If you buy an aftermarket part and it causes a problem, it's YOUR problem, and there's no reason the manufacturer should pay for it. If you are modifying the car, be mature and face up to the consequences if the mods DO cause a problem. (For more help on dealing with a warranty repair, see the SEMA web site.)
It sounds simple enough on paper, but there are lots of fuzzy gray areas. What about a clutch problem on a car running higher turbo boost? What about transmission trouble? What if your front ball joints give out and the car is lowered? Did the lowering cause the problem? Or does it happen on lots of non-lowered cars? Be prepared to make your case, and be prepared for the decision to not be in your favor at times. If you really love your warranty and never want to pay for your own repairs, we recommend NOT modifying your car at all.
But if you want to have a fun time taking a great car and making it better, the way YOU think it should be, and you're willing to take your warranty lumps if they happen, then you're our kind of car owner.
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