I've spent some more time on this, and from what I've found if you revert to stock and pull the battery terminal, the dealer cannot tell if there has been a tune. But if there is a warranty claim the ford tech can come in and tell by looking at the computer.
This seems strange but I've read several post on different sites that all say the exact same thing.
My concern is actually not with the engine having issues with the tune, it's if my transmission goes and they say the tune caused extra stress on the transmission or some BS.
2012 Premium V6 Mustang, Candy Red, Performance Package, Manual.
Mods: Steeda Sports, Koni Yellows, Steeda HD Strut Mount, UMI LCA's, UMI Panhard Bar, Energy Suspension Sway Bar Bushings.