Personally, I'd use Sun Cure. You must know what kind of fiberglass it is though but probably polyester. Sun Cure is great stuff as I've used it for permanent surfboard repair along with using it on the side of my fiberglass TT. My roof is not fiberglass. The Sun cure is of a thick consistency and would be very easy to fill holes in your roof with leaving a slight bit over the hole for a complete seal. Bonds very well when following the instructions. I would never use epoxy on polyester fiberglass. I keep a tube of Sun Cure in my TT in the event there is something I need to repair on my outside walls.
https://www.amazon.com/Sun-Cure-4-4-Fiberfill-Repair/dp/B000PEYSJK/ref=sr_1_2?ie=UTF8&qid=1502126195&sr=8-2&keywords=sun+cure