I have always had tuned Euro cars up until now. I also had a great relationship with all of my Service Managers. I would load the stock file back into the ECU., my bolt-ons, lowering module and TCU tune stayed in place and I would tape up the OBD2 with green masking tape that "said DO NOT ACCESS OBD/ECU". I would also have my SM drive my car into the garage and tell the guys the same thing. He always made sure my car wasn't tagged as tuned. This was done on several of my AMGs, BMWs and Audis.
The first thing I did when I purchased the TRX was go into the RAM Dealership Service manager's office and had a long talk with him. I told him I wasn't planning on doing anything besides Cat-back and Intake and he said that is totally fine. He went on to tell me that they were really tune friendly and how they had just helped a Hellcat owner get his entire engine replaced after he blew it up with a tune.
Go talk to you SM.