I agree, the damage shown from underneath looks like it's about where the trim would sit. Which means repairing it will get out into metal that won't be covered by the vinyl top.
It's going have to taken down to bare metal and repaired, you can try to keep all the repair above the edge that divides the top of the car and the sides of the car, but your going to have find a painter that can blend the new paint to the old in the exposed areas not covered by the vinyl top.
