I know a lot of the VW GTI guys run piggy back units because VW dealers have started going deeeep into the ECU to determine if the vehicle was EVER flash tuned and then denying warranty claims. That has many of them concerned and going with piggy backs instead.
In my research, including talking with service managers at the dealership network that my wife works at, I'm not aware of Ford denying warranty for a vehicle that has been brought in with the stock tune loaded. I'm sure it has happened somewhere, but I have not found record of that.
As long as Ford isn't denying warranty on cars that are brought to them in stock condition, I don't see a good reason to go piggy back instead of custom tune.
Edited to add: VW tuners even reset the flash count to zero when doing the flash back to stock, but the VW ECU still has record of it somewhere. Tuners have not figured out where. Maybe Ford's ECU isn't that sophisticated yet?