I have a 2005 Mk5 GTI. Also having the rust problems under the front wings (above the tyres) - Found after getting my front tyres replaced.
I went to see the local dealer today and they told me it wasn't covered under the 12 year warranty as it is specifically excluded under "trim something"
I took their word for it, got home and checked my manual which states nothing of the sort!
I think I'll give them a call tomorrow with the facts I have - What seems to work for everyone else?
Also, if someone could send me the PDF to read, that'd be great!
Thanks!