Where the Twin outboards were mounted I also had to fill the holes from them. Of course I used the cutout from the new elephants trunk to bung the hole and just sealed round the edges with the filler. If its minor holes and not so extreme like this Sikaflex is very good to seal them.
Any epoxy should do. Epoxy is better than polystyrene resin as it bonds better to various substrates. With holes that small I'd just fill them with thickened epoxy resin.