aftermarket parts only void the warranty if they are the cause of a problem in question...say your mods are a fidanza flywheel, ACT clutch, AEM Intake and Magnaflow exhaust, and your tranny bearings go out...you have no warranty because of the fidanza flywheel and ACT clutch...however if you had a stock flywheel and cluthc and an Intake and exhaust that were aftermarket and your tranny went out, they'd fix it under warranty. To get out of warranty work because you have aftermarket parts, they have to find that the problem was caused by the aftermarket parts on your car.
TRD parts: no TRD part voids the waranty, even the supercharger, as long as it is dealer installed