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Maybe there's a reason, but i just don't understand why a Ford dealer wouldn't have the ability, or would choose not to do it. Unless they are trying to sell you a new PCM instead.
Another dealership has recently flashed a PCM for a fellow member. It's still done, but it's possible dealerships don't want a piece of what comes next. Say you have modified injectors and you flash the PCM to stock. Your truck will run like it's gagging on fuel and idle will be a weird compromise your engine eventually reaches after every throttle use. The dealership's answer will be to return the truck to stock condition to match the flash they just put in. This may run in the thousands of dollars.
I say until you know what's in the truck, you are better off leaving the PCM alone. 0-60 in 10 seconds sounds like new stock to me, and Stinky has done that with stock tuning (before the power modifications) - that's what was in the sales brochure. If you never learn what was done to your truck, all you have is the ability to rotate tunes out with something like an F6 or the Hydra. Try some tunes on a chip that overrides the PCM - starting with a stock tune - and see where that leaves you.
Torque Pro doesn't know what to do with all that torque and a max 3000 RPM - do it calculates 625 HP.