My local dealership has assessed the rust on the two front arches, drivers sill and just under the passenger window. Gave me the usual story about the rust on the arches not being covered as this is a mechanical fault due to the arch liner..we'll see what happens when VWUK get back to me.
TBH I'm not hopeful, but thanks to this thread know what I should be saying to VWUK when they come back with a "no".
One interesting thing that was said which may be of use to other people, rust on the sill is a known problem to VW. Apparently, earlier Mark 5's had two bolts holding the sill to the front wing. These are prone to failure and in later editions were replaced by 2 nickel bolts and a fixing plate. Unfortunately for me, this is considered under the parts warranty that runs for 3 years as opposed to the anti corrosion warranty.