vinyl top or not?

To answer your questions. First, that seam is where the top is actually soldered on, not welded. They are a point of contingency in just about every A body made. They did a super crappy job on cars that got vinyl because they knew it was gonna be covered up.

That said, it's a dirty job, but those seams MUST have all the solder and filler removed and it must be spotlessly clean when you re weld it and do the finish work. Otherwise, moisture will eat it back out like it is now......and believe me it is, whether you can see it or not. Start digging. You'll see.

Second question. The rear window gasket is different from a vinyl top to a non vinyl top car. The non vinyl top gasket is wider and takes up that extra gap. Either way you go, that top HAS to be fixed right or it will rust through again. They all do it. I promise you over 50% of guys on this board that think their cars are rust free would find rust at those seams if they stripped it.