Right. The pressure side hole between the halves, not the suction side between the pump body and block. Maybe Melling has fixed it, but the alignment was so bad, about half the width of the o-ring was exposed to the cover half hole.
And if you are truly interested in improving the flow, or flow efficiency of the pump, you need to start with the block suction side, and at least remove the square inside corner. That is a far greater flow hindrance than that suction block to pump alignment. There are probably 5 places that can use some work in the pump including the pressure side pump to block, although that one is not too bad. But the block and pump passage are on different angles so I enlarge the blend an inside radius. I think even the threaded filter adapter in the Melling had a slightly smaller ID than the original, IIRC.
At the end of the day, thousands, if not millions of these pumps are in service without issue, so they are clearly over engineered enough to make up for it all. But if you are actually interested in making an improvement, correcting that one misalignment is not doing much of anything.