There is no stock answer to your question - it depends. Ford may decide to void the warranty on an OEM part of the car if the part failure is determined to be caused by something you added to the car. Ford does not void the warranty on the entire car at once.
For example, if you change to a very aggressive cam and then have a valve-train failure, Ford may not warranty the repairs to the valve-train, or repairs that are related to the failure (e.g., piston hits a valve, etc.). This does not affect the warranty on your transmission, your electronics, or anything else in the car that is not related to the cam change.
However, there are some activities that could cause them to void the warranty on multiple items. For example, if you are proven to be drag racing the car, you may have a lot of trouble getting the dealer to replace a clutch or a broken U-joint under warranty.