Ford is similar to GM. Non factory ECM voids part of warranty. At least some fords (DS F250 with gas engine) has a big notice on the crossmember by the radiator basically saying non ford ECM tunes will void engine and powertrain warranty.
Perfectly legal for mfg to do as long as it is so stated and in compliance with MM warranty act to so void the warranty.
On GM putting the factory tune back to ECM won't get you out of trouble, since the non factory ECM checksum and other info stays in memory even when you restore factory ECM code.