jomichael,
The seam I filled over was very much like the one you are dealing with. It was a rear corner piece welded to the box. The seam ran vertical, top to bottom. I filled it making the whole side of the box smooth, no seam.
No discoloration to the paint , no cracks, but after 3 years you could see and feel a slight indent the whole length of the seam.
I call that shrinkage, but their are guys that say that can't happen.
For the most part, bondo isn't used this way, which is why I think it never posses a problem.
I think if you were to use filler on the seam you have it would be hard to see it because it's a smaller area and not a big flat area like the side of that box.
I didn't think that would happen over that small seam I filled over, so I threw that caution to you so you would know what could possibly develop in time.
I don't know your time line for completing the truck, but if you are a year away from painting, maybe 6 months would do. Fill that seam right now, rough finish it, let it set and redo it when paint time comes up and that would be a better way of dealing with it.
Dan
