behind passenger side back seat. It's deep and I'm concerned about future rusting. Other than that the car is in excellent condition. How much should it cost to repaint the panel? Also, how much should I leverage with the dealer as far as marking the car down?

 

im suprised the dealership didnt try and cover it at all. i bought my 00 GLE and it looked perfect. but there are a few door dings that they covered up that are starting to show.
repair should be pretty cheap. take it for a test drive and go to a body shop. get a written estimate for repair and take it to the dealership. tell them you want it fixed first or at least that much taken off the price.