Yeah - for a number of reasons:
1. The supply to the core from the engine needs to be connected to the nipple in the intake manifold. This area heats up the fastest
2. It is on the discharge side of the water pump. While the coolant system is actually all at one pressure, the water pump provides circulation through the engine. Coolant is pushed to the heater core by the circulating effect of the pump.
3. The supply to the heater core (like most simple heat exchangers) is designed to come in at the bottom and exit at the top. The reason for this is to ensure that the coils remain "packed" (i.e. completely full of coolant). If the flow is from the bottom up and out the top, any entrained air that enters the coils flows to the top and is carried away. Also if the coolant came in from the top it would be more likely to begin "laning" - following the quickest way out instead of flooding the coils to provide the best heat transfer.
But maybe the best reason is - because the 5/8" nipple is on the bottom and the 3/4" one is at the top.
