wtmr,
Here is what I am seeing...
1) the two holes do not line up at the same angle. The front (second) hole seems to be off-center of the cylinder.
2) the metal flow on the outside of the holes is different.
3) the cut angle of the front (second) hole is not consistant - it changes angles.
4) the two holes have different diameters and the front (second) hole has a changing diameter (like someone rotated/circled the drill bit while in the hole)
I am wondering if the "original finish" appearence is due to the years of carbon build up from gas coming through the hole. Based on all this, I doubt that it was done at the factory and that it got by manufacturer and ordnance inspectors.
As far as WHY? bunch of guesses come to mind... getting a stuck piston out of the cylinder??? .... Bubba trying to make it cycle faster?.... Trying to make it a single-action weapon?.... Who knows, Bubba and "I know what I am doing" military armorers do a alot of things.
Just my two cents...