I would probably just unscrew the screws and then inspect the damage. It may work well to inspect in the evening/night and have a fairly bright light inside the van so you can look for where the light is shining through. (I suppose the reverse might work during the day, looking from the inside, but I somehow think it would be easier with the light shining out.)
If the holes are small, a permanent repair could be made with epoxy mixed with a filler of some sort. A boat supply place such as West Marine would have the materials, though probably not for the cheapest possible price. If the holes are larger, it would be well to put some patches of fiberglass cloth or matting in as well as the epoxy. Do take care if you use epoxy as it tends to be a sensitizing agent for allergic reactions: disposable gloves, good ventilation, etc. are recommended. Once cured it's pretty much inert, though I would not suggest eating it or breathing the dust when sanding it.
Dicor self-leveling would not be good for filling holes or for any non-horizontal surfaces; it's self-leveling because it's rather on the runny side. Dicor non-sag would be better, but I'd probably go with a decent urethane (not silicone) caulk such as OSI Quad Max if I were caulking.
Are the attaching screws on the inside or the outside? If they're inside, no caulk should be necessary. It might be good to put a little bead along the outside of the seam between the van roof and the fiberglass, though I do suspect there would be some butyl putty or something similar there to seal the joint. If they're on the outside, a bit of sealant under the heads might not be a terrible idea. I personally wouldn't bother sealing over the heads, but doing so would not be harmful.
The inside edges of the metal will survive fine without paint. If they're exposed, of course, some sort of finishing treatment would be nice, doubly so if there are sharp edges. (The cut away roof on my class C shows no signs of rusting after about 19 years, and I'm sure they didn't paint the cut edges before hiding it behind headliner material.)