You can still sand the plugs down and glass over them. It's more difficult but certainly can be done. I recommend glassing a small later of glass over the holes first and re-drilling or cutting the fiberglass with a razor blade. This will protect the foam when sanding the plugs flat.Put a piece a masking tape over the slot and screw holes before laminating. After the hotcoat has cured you'll have to cut through the resin and remove the tape.