If the extra holes are under the skin where they won't be visible and won't let air/water into the cockpit, and they don't violate any edge distance requirements, then what's the point in trying to plug them up? Gooping RTV into the holes might not do any damage, but it won't make it stronger either. I would just make sure the holes are burr-free (just deburr as needed, not full on countersink) and move on.