Placing "stock" material in the holes because that is what it was built with is not wholly rational. That is the same logic as if someone never updated the stock chainplates because they are stock, despite proof that older C22's need to have their chainplates updated. Lets talk about this before you go wood plugging those holes. Original is not always right.
If you wood plug the holes, are you going to then fair out the gel coat so that a gelcoat patch extends well beyond the originally drilled hole? Or are you going to simply leave the hole at its current OD and pop some gel in there? IF left at current OD and gel coat to fill in only on top of the wood plug, you WILL crack and you WILL get water in which WILL rot the wood, both the plug and the plywood.
Any time we drill a hole in a boat, we should attempt to remove the wood at a larger radius between the inner and outer skins of the panel in order to fill that region with synthetic material to prevent water intrusion and wood rot. The same should be done here. I think if I were doing this I would take the old mount rails off and with an allen wrench in a power drill, spin the short end of the allen wrench between the inner and outer skin in order to remove some of the wood all around the hole. then tape the inside skin all over to seal it and pack in thickened epoxy filling not only the hole, but extending in all directions a short distance all around the hole, inside between the inner and outer skin.
This will be the corect way to fill these holes, as there should be at least a somewhat solid mechanical bond of the epoxy between the inner and outer skins, effectively sealing the wood from any chance of getting wet from these holes. Then at that point fairing the holes out or not for a top coat of gelcoat is totally a cosmetic issue, not a mechanical one.
Even if you remove the rails and simply replace the old bolts/screws with new stainless scrwes to seal the holes for a fresh, aluminum-free look, I recommend over-drilling, reaming out, re-filling, and then re-drilling. Any time you have a hole open through a cored panel for any type of service, you owe it to the boat to seal the wood from water intrusion...
My $.02
