I found an answer. This is for a different engine but serves the purpose in answering my question.
The main reason the holes are so small is to intentionally create that slight restriction in coolant flow. This engine is designed to flow coolant from the lower radiator hose (where it's at its coolest), through the water pump to the water jackets surrounding the cylinder walls, up through the heads, through the intake manifold to the thermostat, and finally, when the thermostat opens, through the upper radiator hose into the radiator to be cooled. Yes, I didn't mention the water pump and thermostat bypasses, heater hoses, and hoses for the throttle body as these are irrelevant to my point. The main thing here is the flow around the cylinder walls. With the coolest water flowing here first, from the bottom up, and the combustion chamber (the area in the head and upper part of the cylinder) being the hottest section of the engine, the lower part of the cylinder is naturally cooler. With that slight restriction in the head gasket, the temperature of the coolant can be evened out around the cylinder wall water jackets. This achieves two things. First, the coolant is heated up faster, allowing the engine to reach its optimal temperature, the normal operating range. The other thing this does by keeping the temperatures even around the cylinder, is extending the life of the engine. If the upper cylinder is hotter then the lower cylinder, the metal will expand more and create an uneven wear, especially if ran like this for extended periods of time. Eventually the cylinder would be very tapered, causing a loss in compression which means less power and economy, and "blow-by" which means contamination of the engine oil with fuel. The larger clearance between the piston and cylinder wall also allows more oil into the cylinder creating an increase in oil consumption.
