The warranty as a whole would remain, but the following would apply for specific claims related to engine, tranny, drive components:
"7. WHAT IS NOT COVERED BY THIS AGREEMENT: Unless stated otherwise (see STATE SPECIFIC provisions for additional exclusions or changes) the following are excluded from coverage: [...]
b) Repairs to any engine, transmission and final drive components for damages caused by an after-market (non-factory installed)part including but not limited to: turbocharger, supercharger, Compressed Natural Gas (CNG), Liquid Propane Gas (LPG),Nitrous Oxide fuel system modification or any other performance enhancing powertrain components including but not limited to racing parts or accessories; [...]
e) Failures caused by: (1) alterations or modifications of the Vehicle, including the body, chassis, or electronic components, after the Vehicle leaves the control of the manufacturer (2) any part designated for “off road only’’ that is not installed by the manufacturer, including, but not limited to, lift kits, oversized tires, roll bars, and performance enhancing powertrain components; (3) tampering with the Vehicle or the emissions system and components; (4) installation or use of any mechanical or electrical part not approved, certified or authorized by the Vehicle’s manufacturer or any Failure caused by after-market(non-factory approved) PCM reprogramming;"
In practice, if you have a dealer that is willing to not point a finger to the tune as causing the failure or damage, it should be OK for these types of claims.