The trim won't cover the seam. It appears to sit correctly in your picture. Originally the window plug has a thin insulation-like material glued to it. The vinyl is not actually glued to the plug, it is only glued to the metal, and stretched over the plug, and glued in the window channel as well. At the bottom, on the dutchman panel, it is only glued to the edge of the panel under the trim. In addition, there is a thin stainless strip (3/8" or so wide) that is screwed down to help hold the edge of the vinyl in place. This is all covered by the trim.

This is what I found on my RT SE. It had original paint and top before I restored it. Attached are a few pictures with some measurements. Unfortunately I don't have digital pitures of it when it was all apart.