So, I guess the main thing is that the dealership is capable of removing whatever tune is installed and return it to stock. Then you could load whatever other tune you'd want. That's what I would do for sure. Someone may have loaded some WILD tune that you may not want anyway......
When i traded in my last mustang I left the aftermarket tune on the car because it had headers and no cats. The dealer called me asking if I would come and reflash the stock tune back on the car. I thought they were crazy but i did it anyway since it allowed me to use my SCT tuner on another car again. Salesman said it has something to do with Ford charging them for another tune but not sure if he actually knew what he was talking about.