We see a lot of customers with Turbo's, S/C's etc. When warranty work is required, unless they can CLEARLY PROVE that the addition of the aftermarket parts caused the problem, they will be required to cover you under warranty.
Latest example? An Dodge SRT4 with a larger turbo, intercooler, Spec Clutch and much more. We sent him to his local dealership where he bought the car when he had a drivetrain problem. His dealership covered it under warranty. Under the Magnuson Law, it is pretty difficult for them to deny you service although they will try.