I’m afraid what you have is Galvanic or Bimetallic Corrosion. This was Not covered by the 12 yr Anti Rust warranty which refers to perforation of body or chassis components from the metal outwards.
What you have is different and was originally only covered for 3 yrs from new later increased to 6 yrs for T5/5.1 vehicles only.
Also, in all honesty you do not want to have the latest repair that VW carry out. Many who have now regret it.
You would be better off finding a body shop that specialises in vehicle restoration or bespoke vehicle repairs repainting and get the affected areas rubbed down, high content Zinc primer, filler and respray. Last price I saw for that was about £550.
This repair would probably last 5 to 10 yrs or longer.