The theory was that dealers/collectors did not want stamps with holes punched in them. They had to purchase intact, unpunched stamps (in full panes or quarter panes) at the philatelic sales counter at a 10% surcharge (20% for postage due stamps).
Here's an excerpt from Mr. Leslie Ettre's article published by The Perfins Club:
For most of the issues punched, the two middle rows had the three holes, however, the Harvesting Wheat stamps had the two middle columns
punched (again, credit to Mr. Ettre):