The reason I go to stock before letting the dealer work on the car is partly an SCT lock issue. When you load a tune into your car the stock tune is loaded in the tuner and saved and the tuner is “ locked” to your car.
If the dealer flashes software different in the engine there will be a mismatch and you won’t be able to return to the original stock version.
Then tuner considers itself locked and has to be sent away and unlocked by SCT for a fee, and you would call Pete, he emails you the dyno tune if he kept a copy and you start the process over again.
If the car is behaving as normal I wouldn’t worry - I just am a bit paranoid on software flashing, have seen a few horror stories in my line of work when things didn’t go as planned.