Wouldn't hurt, woldn't hurt to waxoyl it between the arch liner and the arch itself either.
As I understand it though the failure starts because the arch liner moves ever so slightly going over normal bumps / engine vibration etc and eventually wears though the paint. This in turn lets the water / crud that makes its way up there attack the bare metal. Maybe worth putting some sort of anti friction tape up there if the paint is still sound.
Anyone have any idea if A3's are affected with this problem? I think Leon's are but not sure if the arch liner design is different for A3's ...