The original pistols I've seen with the holes closed-up under the finish were probably originally rejected and sent back to be repaired prior to shipping. Some of those pistols do not have any final inspection or Ordnance Acceptance marks, but have what are believed to be factory repair marks on top of the receivers. There is still more to learn about how many pistols may have been defective and how they were repaired.

Those original pistol repairs were neatly done with what appears to be specially made punches shaped to go around the edge of the hole. They don't looked all Bubbafied.