First off a Warranty Cannot be voided... period. As far as a tune goes, its no different if you slapped a Supercharger on top, you are changing the Factory specs of the car from what Ford Engineer's programmed it to be. If you blow the engine, Ford can easily see if you have a reprogrammed PCM, that is if you leave it in there for them to find it. When it comes to warranties, Dealers don't make much of a profit on repairs. Ford loses money everytime you make a warranty claim. Dealers are independant of Ford, thats the reason why Ford can't set a car's price. Now lets say you did tune your car and leaned it out to the poitn of death. If the dealer can tell that you changed the programming they can deny you a warranty claim on the engine. Now if you bring in your car for something else, lets say the door locking mechanism doesn't work anymore, you are still covered under the warranty. Think of the warranty as the whole car. If you cause the damage then they will choose not to repair it. Anyone can try to fight back by going to a regional Manager where you may enter arbitration, IE get a lawyer or hope it goes in your favor. Remember the dealer has nothing to do with Ford, so they are a seperate party.
The other thing about aftermarket parts is that lets say you get Ford Racing parts for you car and have them installed by your dealer who says he/she will cover you under the warranty. That ONLY applies to that Dealer and i would get it in writing. A Dealer cannot say that Ford will cover the aftermarket parts as they aren't Ford and don't have the authority to answer for Ford. The dealer can do what he want, and many are starting to get into the performance side of the game so they can make money. The Warranty only covers what exactly left ford's factory. You can take your car to any Ford dealership for warranty repairs. Aftermarket parts can only be warrantied by the dealership where you had them installed and have a binding agreement between you and the dealer or by the company that made the part (ie some superchargers have 3 years engine warranties) if its covered.