To void your warranty Ford would need to prove that your modification caused the damage you are having the vehicle serviced for. Even then, the warranty isn't voided, it just won't cover damage caused by modifications you made...it'll still cover other issues with the car.
2012 Focus Ti Hatch, Blue Candy
2011 Mustang GT, Grabber Blue, 6spd
1978 Mustang II, 351W, Tremec 3550
1978 Mustang II, 2.3L Turbo, 5spd