Unfortunately if you tune (pcm swap to tuned one) and get a warranty flag it gives the dealership a bit of a get out of jail free card on electronics and powertrain (sytems impacted by tunes) when it comes to anything covered by the Magnuson Moss Warranty Act.Unfortunately the "we did nothing to cause this, whatever is in the work order is a misprint we didn't do it because of the code and your mopar certified exhaust needs a tune so tell the installer to clear the code and remove the tune we cant find of prove that you have" talk from the dealer after 3 weeks of having my car doesn't inspire much confidence. Then the threat to void my warranty and Dodge srt telling me well the dealer said what they said and there's nothing we can do about it because we don't know about cars so we have to believe the dealer!? oh and the Merick service director telling me that I brought the car in like that "we didn't look at the dash so it was probably like that. its like going for an routine operation wake up and realize you missing a kidney and they go well maybe you came in without one and now you blaming us... this is so ridiculous that this people deserve some time of lawsuit to restructure the way they do business.
Once you are flagged Stellantis and every dealership knows this so you're fighting a way uphill battle.
You're not only going to face this relatively minor (non driveability related) issue possibly not getting resolved but you are getting a preview to how any more significant issues down the road will be handled.
You're likely much better off going to independent shops that specialize in mopar at this point since its not a warranty issue (at least they don't feel it is).