Over the years I have seen a few variations in the size and placement of these holes. However it always came down to getting the correct amount of coolant through the motor at the correct locations to get even temps from front to back. The later gaskets have this figured out as to hole location and size.
Engines with the water inlet and outlet on the same end must have staggered distribution front to back for even cooling.
When and how this was figured out I don't know, but it work good.
