Very common on the sills due to this mess that builds up behind the arch liner:
If you're asking if vw will knock some money off or do it for free then I think you're going to be disappointed. You can just replace the wing for a 2nd hand one or buy a new one and paint it, not a big issue. For the sills, on mine at least om going to have to remove the doors to be able to get to it and remove the rust and paint the area/blend it in.
If you want a good quality job and not just d.i.y it so its OK then I'd find a local body shop with good reputation and get a quote frankly. You can always try VW I guess but I'd super super surprised if they even entertained the idea.