From watching folks use "bondo" (automotive polyester body filler) as a repair compound I found the experts were correct. Polyester repair resins are not "waterproof" and in the long run are hydroscopic.
Gel coat is used for two main reasons. It forms a smooth surface (and remember most gelcoat is the first layer in a mold) and even though it is polyester based it serves to waterproof the underlying polyester construction resins. Ask any boat person about "blistering" which is moisture getting between the gelcoat and resin layers and forming delaminated areas that resemble blisters.
The fix is to grind them out and replace with epoxy that will both bond and form a waterproof repair.
As for ABS repairs there is a company that is now producing a specific repair package for ABS using an epoxy resin, but like it was noted; Acetone is added as both a solvent for the ABS and the Epoxy so the two dissimilar materials will actually form a "welded" bond. It's not cheap and not really designed or cost effective for large area repairs.