Similar issue on my bus. I thought about doing it your way but there were too many cracks on the surface of the seam material. I used a sharp chisel to shear the whole seam material off off, then filled the gap with sikaflex (or equivalent), letting it cure, then screwed a piece of aluminum transition over the joint with enough sikaflex to squirt out the sides. It's a pretty clean look, so if your first efforts still give you trouble, don't be too afraid taking a more invasive approach.
While the seam was exposed I also sanded the fiberglass down to a clean white surface so I can wax it in the spring.