Sorry for this long answer: If you replace the PCM there will be a difference in the mileage recorded on the PCM vs. the mileage on the speedometer if you switch back to the stock PCM. While I haven't ever heard of a dealership doing this there is still a discrepancy in the mileages recorded. That may be one way, at the dealership level, they could check to see if the PGM has been replaced. My personal opinion about these tuners and the effect they have is if you drive the **** out of your truck, race stoplight to stoplight every day and then go out to the drag strip every weekend and beat on your truck a 1/4 mile at a time, I'm sure sooner or later you're going to have issues. If you drive reasonable, getting on it every once and awhile but don't beat your truck to death, I think you and your truck will do just fine. I think you'll have to look long and hard on this forum or others before you'll see someone that got into a real fight with a dealership regarding repairing a truck with a tuner. I'm sure you might find some instances but it sure doesn't happen very often, that I know of. Talk to your dealer, establish a relationship with the service writers and the service manager and see what their attitude about tuners is and see if they will work with you if you have a problem. And start the conversation BEFORE you have a problem.
Jay