I would guess they were correcting for a casting flaw. Note how the stud holes are offset also compared to the outer part of the flange but centered on the modified holes. Not uncommon, my buddy had a Stromberg head that the front part, ahead of the timing gears, was bent inward significantly but they drilled the front, small bolt heads in it and it worked, just barely. Must have been a 1/4 inch offset.
Jerry Rude
4005R