I have this issue at the moment on my 05 GTI. I noticed the rust coming through about 6 months ago but thought nothing of it until stumbling upon this post.
Today i thought i would start the process of trying to get the issue sorted under warranty, First step i phoned customer service and was told to take it to nearest paint shop which i did and spoke to a very helpful salesman who informed me that he was aware of the front wheel arch issue but had no knowledge of the sill issue.
While inspecting my car he went to the wheel arches and said he was willing to compile a report as the arches are showing signs of rust which will be under the 12 yr warranty. on which he took photos of the areas L/H & R/H.
When back in the showroom he went onto VW database and brought up the issue regarding the sills and showed me pictures of other cars that have had the same problem, (Fixing bolt from front wing to sill) causes this and said that it isnt covered under 12 yr warranty but has put in a good will claim which is a sliding scale on age,mileage of vehicle, which turned out to be 50/50.
I got home and informed customer service and told them all about what had happened and was told they would call me back.
2 hours later i received a call from VW informing me that the cost of my half to repair of the sills would be £280, which i found totally unacceptable and told the adviser to take it higher, which is where i am now.
Could anybody give me some advice on how to get this under warranty?, any info would be greatly appreciated.