Filling Drill Holes in Fiber Glass Roof

since I haven't gotten an answer yet I will "assume" that the area is accessible from the bottom. in that case I would properly rough up both the inside roof surface and the surface of a disk of fiberglass or some material that is waterproof. I would then epoxy small disks of that material under the holes. when done properly that will permanently "fix" the holes other than cosmetic issues. then I would take white bondo or similar material from a marine supply place and gradually fill in the holes, finish sanding to make level and spray with white enamel.
this will be largely unnoticeable and you won't have gobs of tape, etc. hanging on the roof.
bumpy