It comes down to convenience. Would you rather put in the time and effort to sell it on your own for a couple grand more? Or, do nothing and trade it in for a couple grand less.
What is most likely happening is that the auto down feature, when you open the door, is not working. This effect will position the window outside the seal instead of under it. Lower the window and raise it with the door closed and it will seal correctly. Let the dealer know the auto down isn't...
Town Fair Tire did the same thing to me. I brought my new rims to the appointment and they wouldn't install them even though I bought then tires from them. Took everything to a local shop and they did it.
That is insane. I would go public with your story and tell the dealer you will be exposing their customer abuse. Don't just let them screw you and get away with it.
Hey. Since you have to fix the door anyway. You could slightly hammer the edge of the door in, at the point where it contacts the fender, so it will clear the fender. Better to ad a little more damage to the door then the fender.
The scratched around the lugs will happen but not the scratch next to it. The worker had no clue and was taught how to separate the UPA from the knuckle. I would insist on new UPAs and have them installed somewhere else.