I had a similar situation with my last car - a paintwork blemish on the nearside sill that looked like dirt under the paintwork. The dealership said they’d get it repainted, but I wasn’t keen to have part of my brand new car resprayed. The car was metallic blue so the whole sill would need repainting and blending into the rear wheel arch, with the risk of paint shade or paint finish differences between the original factory paint and new paint.
I decided to leave it as it was. For the first few weeks, I couldn’t ‘un-see’ the blemish - it was the first thing I looked for whenever I walked up to the nearside of the car. However, after a while I forgot about it, and didn’t even really notice it, even when washing the car.
Of the five VW’s I’ve owned, four have had either uneven panel gaps or a paintwork imperfection. Some I’ve had rectified but others I’ve lived with. So much for VW build quality - my current VW may well be my last………..
If I was in your situation, whether or not I had the blemishes rectified would depend on how large they are and whereabouts on the doors they are. I’d also be asking the dealer what the risk would be of paintwork colour / shade mismatch - Moonstone is non metallic so it ought to be relatively easy to get a good colour match, although the quality of workmanship is ultimately down to the individual body shop employee doing the work.
