It's pretty easy to tell on all the newer diesel, even the 6.0. You simply pull up the date of the last re-flash, and if the firmware version at that last re-flash wasn't available from Ford at the time of re-flash, then it means it was "restored" from a tuner.
I had a low-mile 6.0 Excursion in my shop for one of my dealer customers, fresh from auction. It needed the full Head-Gasket and both coolers, but with the bad head gasket, unknown full history, and being unable to verify compression, I had to tell them it may need a full replacement. With the diagnostics printout (AutoIngenuity) they were able to get the auction company to buy it back because it was sold as "stock" at the auction.
OTOH - one of my friends took his EcoBoost in for the intercooler update. This involved a re-flash, but they didn't tell him first. He was running a 5-star tune. He called them to ask why the truck ran different after the intercooler, and they apologized for re-flashing without telling him, and gave him a free oil change for the inconvenience of having to re-load the 5-star. So... apparently Ford isn't cracking down on tuner on that motor (yet).
