I haven't had to argue a warranty issue before since I've never modified a vehicle's powertrain while still under warranty, but how exactly do they "prove" it was the tune. Sounds like they could just say "our tech looked at it, it was xxx (such as engine stress) and we believe the tune caused it", and you're SOL.
The techs computer can show the cause of failure. Case in point, if they see the issue was caused by the car running lean then that could easily be pointed out as part of the tune. It has to be an issue pinpointed by Ford and directly connected to the tune. You don't have to prove it was not caused by the tune, Ford just has to prove that it is.
2014 5.0 Base 6MT Sterling Grey w/ 3.73's - OptiGuarded, FRPP TrackCal Tune, Boss 302 Quad Exhaust with Ford Racing GT500 Axlebacks, Barton 6-Speed White Ball Shift Knob, MMD Classic Quarter Window Louvers, MMD Decklid Panel, MMD Ducktail Spoiler, Boss 302 Grille w/ Foglights, MGP Caliper Covers, Craven Speed Stubby Antenna, JLT Oil Separator, Boss 302 Strut Tower Brace, Roush RTR Rocker Panel Splitters, Tri-bar Wheel Caps, Front Splash Guards, & WeatherTech Laser Cut Floor Liners.