Hey chaps,
After some useful help on here regarding the rust on my newly acquired Jetta I took it into VW today for it to be looked at. The warranty administrator Kevin came out and took many photos of my car including the problematic areas which are currently
Boot
Bonnet Edge
Sill where it meets arch.
He took paint depth readings which I was thrilled to see all are very consistent across the car. Here's hoping I have some joy with VW taking care of this.
I want to thank you all for your helpful advice so far. This is possibly the best and most active VW forum in the UK that I've come across also :)