Nothing will void your warranty unless....
..... the modification you made was the cause of a failure. If you installed twin Turbo's and jacked your engine up to 1500 hp and then your brake master cylinder failed, it would be covered because your engine modifications had nothing to do with the failure. If the crankshaft failed however they probably wouldn't cover that. If you add an Accufab exhaust, tune, and pulley, and your half shaft bolts fail, or an oil pump fails, or your power window goes out, Ford will cover it. If you fry your car's computer in the process of re-flashing it, you're on your own. No manufacturer will look for an excuse to void your warranty for modifications that did not cause a failure. On the contrary, it has been my experience as a new car dealer that many repairs were covered under warranty that clearly should not have been.
Chip