The factory, untuned, unmodified, untouched computer programing is not always the same. Ford has done a few updates from what I understand. the way to get these is by reflashing your computer at the dealership, or i think Bill has a way of doing that as well, but IDK for sure if he can do that remotely, or if the gryphon already does it. I do not believe the EVO has that option.
If you programmed your truck's computer, then returned it to stock, it should have returned it to what you had unless it was set up to program a better program from Ford given to you by the Gryphon through Bill, but like i said IDK how this exactly works because the diesel and gas stuff is so different, and my F-150 doesnt come with diesel

If you are talking about the canned tunes, then yes the stock canned tunes inside the gryphon are different from the evo. Bill works a little better magic for his customers than for edge's customers

.
I hope this answers more questions than it creates

.
__________________
2002 F250 MT, Bill's 100hp custom tune on the PCM, Phoenix: stock, 45hp, 65hp-wm, 80hp-wm, 120hp, and no start. pioneer nav radio, 12" memphis sub and 500W amp, infinity 5x7's, alpine 4-ch amp, stock front speakers soon to be focals
2006 Mustang GT, SCT XCAL3 91 tune, custom tunes soon, pioneer nav radio with a JL Audio W3 12" sub and a jl audio jk3602 amp. Speakers and amp soon