I checked mine and I have a line in the same place as yours but no rust (yet)!
Only thing I can think is to pursue a claim that it is a major design flaw and SEAT's fault
It is only where the inner seal is on mine, so I think it is from the door and possibly made worst if the paint is thinner there. I'm thinking about going over it with lacquer while it hasn't rusted to give it a bit of extra protection.
you could fill it with touch up paint, wait for it to dry (at least a week), wet sand the excess off and buff it back to a shine using a da polisher. This method works well with non metalic colours and it's actually quite difficult to see where it's been touched up.