Back when I had my '70 Westfalia, I pulled the windshield and the rear quarter windows to do some paint work and found rust on all the lower edges of the window frames.
I wire-wheeled it off (some of the area around the windshield was pitted, but none of it was all the way through), applied some Permatex 81775 rust treatment(RT-8A), and then painted over the area (which was the purpose of the project anyway).
It worked well for my situation, but I was able to remove my windows and treat the whole area.
If you are able to remove yours, I would recommend this method because it's fairly easy, it's inexpensive, and it works.
If you can't remove your windows...
I really don't know what to tell you because you really need to treat the source, which as Uncle_Fester said, is likely to be that unpainted, cut edge.
Besides, If there's rust peeking out from behind the seals, there's likely to be much more underneath the seal that you can't see.
(My VW never looked rusty around the seals. It was all underneath.)