A body axel with multiple holes

Why would one go through the trouble of re-drilling and not utilize them? I would question if the 4.5" bolt circle is off. The bolt circle or index being off a bit could make it real tough to get the lug nut shanks through wheels.
Then too, maybe the re-drill was meant for future mods.
This axle was plugged prior to re-drill. The studs are 1/2" X 20R X 2" grade 8 screw in.