Ok, here is the deal.
According to the Magnussen-Moss act (see
www.sema.org ) your warranty cannot be denied simply because of the use of aftermarket parts on your car. The mod must be proved to have been the cause of the failure that they are denying your warranty on, nor does it allow for the entire warranty to be voided, just the parts affected by the mod that cuased the failure.
Unfortunately, in the real world, most of us don't have the time, money, or legal counsel to make that stick every time a dealer wants to be a jerk about it. The simple fact of the matter is, you are best off finding a dealer that is knowledgable and very up-front about modified vehicles if you plan on being able to count on warranty service. Honestly, I have seen some pretty jacked up warranty denials, that really should not have happened, simply because the dealer was being a jerk.