This issue seems to be more common now, as you'd expect as time goes by and cars get older. As far as I can tell, the preventative measure of fitting the arch liners was only done on the VW Up! for facelift models (as a "product enhancement") and so anything else, especially an earlier car, needs to be approached with caution. Newer cars could have some remedial work and preventative measures but for older cars it may be too late.
I am wondering how willing VAG are to step up and address the issue under warranty as there seem to be very mixed experiences for owner who have raised it and if every car starts to suffer they could be taking a big hit? It appears the full fix is about £1k to implement. Given it's a 12 year warranty every car is in scope.
Finding decent cars is always tricky, this little feature adds a further complication and depending on the above makes me wonder whether to call off the search. If this issue is a question of "when" and not "if" then it's really off-putting.