The smaller holes force the water to circulate around and to the ends of the block. Like little geysers. If you open them up. The cooland will just lay undisturbed in the bottom or ends and not move the absorbed heat out of the block.
I have already had a customer open the holes up on a Big block chevy. Trying to improve the cooling in a suburban. The motor overheated in about twenty minutes and would not cool. A lot of my shops time was wasted trying to find the problem. As we had done the machine work (not the assembly).
Customer was not happy with the billing, after it was found that he caused the problem.. So don't screw around with something that has been proven reliable since 1955..