Ok, to state they know its a PPE lvl4 tune in there is far fetched unless they had the tuner that put that tune in the truck. No scanner or tuner (besides PPE) can tell you what was in it.
Next, ignore the fact they claim its a PPE tune that was in the ECM. EFI Live only makes changes to factory parameters in the ECM to benifit the user in what they desire for power and/or drivablility. It does not come with any preloaded tunes unless the tuner built some. If someone used EFI Live to retune the truck, they could have a done a few things.
1. Made some tuning changes to the orginal tune that was in your truck. If that was infact a PPE tune, it still is a PPE tune with tweeks done to it. Its not a 100% new tune and is not a "stacked" tune. parameters inside the tune were changed from what PPE made. you would have to know eveery single table PPE touches and change them around or put stock tables back in place for it not to be a PPE tune.
or
2. they flashed in a new stock tune via your vin, took that tune and made you a new tune off that, then flashed that in (this would be its own tune and have nothing to do with the tune that came out of it unless they copy/pasted from the old tune)
Also, there is no set HP limit on the allison, stock or built. You can not say "jim" can load a 90hp tune in his allison and go out and never have an issue with it due to power. tuning, driver, and a whole lot of other factors play into the roll on just how long a trans will last before a limp or worse. ANYTHING over stock hp reduces the life of an allison. Sure you can keep your foot out of 5th gear to keep it from limping but if your running that big a tune that it will limp that easy in 5th, it wont be long before your other clutches are toast inside or you loose a converter and you go nowhere fast.