I’ve read on other forums in the past of instances where these milky white blemishes have appeared under the clear coat on new cars. They do often disappear, but not always.
These blemishes are a characteristic of moisture trapped under the clear coat. This can happen if a car has been painted in less than ideal conditions before the clear coat is applied over the base coat, but it shouldn’t really happen when the car goes through the painting process in the factory as the environment is very carefully controlled. I’ve read that some car manufacturers also use a ‘flash heat’ process to remove any moisture from the base coat before the clear coat is applied (I don’t know if VW use this process) and before the body shell then goes through the ‘oven’ to bake/harden the paint.
In the OP’s situation, it might be worth speaking to a professional detailer as they’re likely to have seen this before, and they will be able to advise the OP on how likely it is that the blemishes will disappear permanently over time. The fact that they’ve reappeared after the dealer fix suggests they might not disappear. A detailer can also measure the paint thickness with a PTG (paint thickness gauge) and if this reveals paint that is thicker than expected, this would indicate some repainting work may have been carried out since the car left the factory.
If the issue is moisture under the clear coat, I wonder if the dealer fix was to put the OP’s car in the low bake oven in their body shop in the hope that it would dissipate any moisture permanently?
OP, please keep us updated of developments.