not exactly sure where the hole is. there is a portion of the transom that is solid fiberglass which is the area around the drain plug. you will see this area as the transom gets much thicker where it is cored with wood.
if the hole is through the transom that is cored with wood, then i would remove all of the old sealants and clean out the hole with a drill bit. then wet out the exposed wood thoroughly with some quick curing clear epoxy resin. let cure completely, then fill the hole with some white Marine Tex or similar product. use blue painters tape on one side of the hole to help hold the Marine Tex in place while it cures. on the outside of the transom leave the Marine Tex about a credit card thickness shy of filling the hole. after it cures, rough up the Marine Tex with some 100 grit sandpaper. lastly, completely fill (slightly over fill) in the remaining thickness of the exterior hole with some Parker gelcoat. let it kick, and then wet sand (400/600/1000/2000) it smooth with a small sanding block about half the size of a deck of cards. polish and then you are done.
if the hole is though the solid fiberglass part near the drain plug, then i would not fill with Marine Tex because the matl is not thick enough reliably hold a plug. in that case i would have a professional fiberglass it in which is going to leave a larger defect to gelcoat and sand.
