I'm no expert but I don't think that hole is part of the program. It looks to me like the casting was thin in that area and broke through while machining. I imagine the floor of that hole is thin as well.
Judging how the pump works, I don't think this will affect anything.Or might it?
I was born with nothing and still have most of it left.
Just checked one of my upper case halves and that square hole is there too! It's not machined in, it's cast that way. Probably a drain hole to allow any oil that comes up around the pump drive when it's turning to drain back.