I had this problem on my Caravelle, it only use to rub the bodywork if the door bounced while closing, (they were fully electric doors) I reconed at the time to adjust and tighten everything I could. My Caravelle was out of warranty so my resolution was to pack out the channel the guide runs in with a couple of washers (just before the guide bends inwards). Because of the angle of the panel etc this gave me a good 2-3mm of extra clearance. This worked well for me and I then got the panel repainted! That said, if it’s under warranty just let VW sort it