Advances timing, changes air fuel mix and "maybe" shift points...not a lot of modification being done. You can also take it out and plug the cable in its slot before taking it back to the dealer if you encounter engine issues...
The stock SRT-8 at WOT 3500rpm-reline runs at high 11:1 of 12.0:1 AFR.
Believe it, there's a lot that can be done even in stock form.
Any modified car needs to have its EFI customized. That's just the way it is. Imagine if you had a carbuerated hot rod and could hardly adjust any carbuerator settings. It's the same thing.
Start adding head work, cam, valve train, throttle body, intake, etc....and you really need to edit your own EFI.