The Magnuson-Moss Warranty Act states:
"The federal minimum standards for full warranties are waived if the warrantor can show that the problem associated with a warranted consumer product was caused by damage while in the possession of the consumer, or by unreasonable use, including a failure to provide reasonable and necessary maintenance."
So basically they have to "prove" your use or modification caused the failure. If you put a K&N on there and then suck water into your intake and hydro lock the engine they could possibly "prove" your modified air filter let the water in where an OEM filter would not. That would be your loss. If you lift your truck and put 33" tires on it and it drops a valve they cannot void your drivetrain warranty because of your lift mod.
http://en.wikipedia.org/wiki/Magnuso...s_Warranty_Act