No it will not automatically void your Ford warranty. First of all, when you tune your vehicle, the SCT Tuner stores the stock file onto the device. When you are going to go in for Warranty work, you can return the computer to stock settings. The SCT tuner, unlike other brands, leaves absolutely no footprint in the PCM history. In order to deny any warranty repair the dealership has to prove without a doubt that the Programmer was the cause of the damage. We can thank the Magnusson-Moss Warranty Act for this.
If you are overly concerned with this topic, talk to your dealer. Ultimately they are the ones that will make the decision.