Don't get confused here. This is a particular case where the inlet nozzle of the MCW6000-A is performing slightly better than the inlet of the MCW6002. 3/8" tubing IS wasting finite pump head that could be used to generate water velocity in a block. Whether that matters is going to be pretty personal: some people value tidiness and quick disconnects more; some people want every last fraction of a degree in cooling.
Personally I wonder how well that the MCW6002 would do if it had an inlet nozzle that tapered to closer to 1/4" ID and but still used 1/2" barbs. Would the increased water velocity make up for the decrease in flow rate?
I'm sure Bill knows...
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