Rust where? On the wings?
They definitely get replaced so long as the paint depth test is a pass. It doesn't have to have a dealer history to qualify. The paint depth test is going by the theory that humans can't spray as thinly, or as uniformly as robots, so is a good sign of accident damage.
If the car is rusty elsewhere, such as a tailgate, sill, or panel other than the wings, your chances are slim I'm afraid.
That kind of blanket "Get lost, we're not interested" letter sucks. How do they expect people to buy another VW (which is what they want) based on a response like that?