Ford will not hold up the warranty if you install something aftermarket and that causes damages to a part that is covered by warranty. An amp wont really void any warranty. What it can do is cause a void of warranty on audio related systems like a sub or speakers for supplying to much power to...
I had a brake squeal from the fronts after about 3K on my 2016 GT PP. Only happened sometimes, while braking, at any speed. Took it to the dealer. They cut the front rotors and put on new brake pads. 4K since and no brake noise once so ever!