Just because you install a tune in your car it does not automatically kill your warranty. Ford has to prove that the aftermarket part was the cause of failure. Now if you do install a tune and something goes wrong with the engine then yes you probably won't be able to use the warranty for repairs. It depends on the part. You still have a lot of other parts on the car that are still covered by the warranty.
AED and Lund are also good tuners from what I have researched on this forum.
2013 GT, Track Pack
, Recaros, Kooks Axlebacks, Airaid CAI, BMR Rear Adj. LCAs, BMR Relocation Brackets
, JLT Oil Separator(s), Barton 2 Post Shifter Bracket
, Steeda Motor Mounts
, Barton Shifter
, JHR Clutch line, BMR adj. UCA and Mount, Kooks 1 3/4 headers/catted H, DSS Al Shaft
, BMR Loop
, Vogtland Sport Springs front/BMR rear, Strange Adj. Struts/Shocks, Extended ball joints, Steeda Bumpsteer Kit, Whiteline Tranny Mount Bushing, Borla Overaxles, BMR Watts, Vorshlag 3" Ducts