It sounds like they are trying to take the mickey. They shouldn't have had the car for 2 weeks initially- once they realised the car needed new wings, it should have been returned to you for you to use whilst they were waiting for the new wings to arrive and then been taken back in once they had arrived. The wings should have been prepped prior to fitting- ie rust proofing on the inside etc, fitted and then sprayed once fitted and aligned correctly on the car. If they have done the job properly then you should not be able to see that the panel or panels have been painted. A good body shop takes pride in their work.
The body shop I use told me a story of a brand new civic type r that was pranged and the owner let the insurers recommended body shop repair it. When it was done, the owner picked it up and was horrified at the standard of the work that had been done. The assessor came out to see it and agreed that the repair was well below standard. The car was then sent 60 miles to the body shop i use to repair the repair.They had to remove the wing and door, re-fit them, prep them and respray them. The owner of the car came down to pick the car up, and was like a child at christmas when he saw the car repaired properly. The first garage is no longer recommeded by the insurer!
My advice is to take the car to 2 independant body shops for opinions on the work,possibly get a written report on the fit and finish of the job, and return to vw with your findings, and take it up with the most important person you can get your hands on.
Good luck