Just to be clear, a tune does not void your warranty. However, it can give the dealer a chance to deny a warranty claim if they feel the tune caused the failure. In other words, if your power windows stop working, a dealer would be hard pressed to deny your claim based on a tune.
The PC does not leave any trace, so you are less likely do have a warranty claim denied. With all of that said, I would spend a little more money and get the MPT 93 PRX tune. It will really wake your truck up and does not require any mechanical knowledge on your part to install or operate.
To clarify...Any aftermarket tune will void your powertrain warranty; the manufacturer is not responsible for engine/trans/driveline issues once the factory calibrations have been overwritten. As for concerns like the power window example you provided, you are correct. The warranty on unrelated systems is not affected.