I have an Astro roof car that I brought from a board member that was exactly like that, maybe a little more. I did have that area blasted to make sure that nothing was missed or would show up down the road. I have never seen that issue on a hard top car, odd. I wonder if it was an issue of whoever was making the astro roof skin. The body shop actually used tin/lead to fill in the tiny holes. Once it was sanded flat, primed and painted, you cant tell at all. That was 4 years ago and that body was put on hold, I finally got the astro roof panel weatherstrip seal and will get a new headliner and a few more interior pieces to move onto the next chapter on that project. I love seeing the miracles of metal workers and I am sure that it can also be cut out and replaced and look perfect as well. I can try to find pics of what mine used to look like.