I refused to buy my EOS unless the dealer got the mirror mounts fixed. They replaced them under the 3 year factory warranty (phew). When the Stealer tried to sell me their VW approved Mondial extended warranty I passed it over as it did not cover roof leaks so I suspect your warranty may not cover paint finish.
If you recently bought, I would try your dealer first. In my case the car had come from a seaside area (salt water!) and that may have accelerated the paint bubbling.
When I looked at the damaged items I could see the mirror mounts were diecast aluminium and their paint finish looked like a single coat electrostatic spray over. Not the process of base etch primer and top coats I might have expected for aluminium parts exposed to weather.
Since my mirror mounts are black, they could have been removed, acid etched and properly re-painted or powder coated after etching. I think removing the mirrors requires some work so I was glad the 3 year VW warranty covered it.
The big question is did VW change their paint finish specification on my warranty replacements, or will they go the same way? So far they have been ok. Personally I found the corrosion very visible and ugly. I would get yours fixed either by the dealer or have them re-painted. At least you should never see that annoying problem again.