Ok - flow rate (as we typically measure it) is gallons per hour. Assuming a constant flow rate of 1 gallon per hour, it's quite obvious that the speed of the water in a 3/8" tube is MUCH faster than the speed of the water through a 1' diameter pipe. Now I know that flow-rate could also be interpreted as the rate of speed at which the water flows, but thats not what I meant above - I'm talking volume per time flow-rates.
As for a small channel slowing down the whole system, of course it will. But one small section of an entire cooling loop does not dictate the resistance to flow of the entire system, regardless of the pressure of the system. The entire water-cooling loop will have a certain value that reflects how much it resists the flow of water (in an electric circuit it would be ohm's, I have no idea what the unit is for resisting coolant flow). Then there is a pump providing pressure (in the electric circuit, you'd have a voltage from a battery/PSU). With knowledge of those two things you can calculate flow-rate in gallons per hour (amps in the electrical circuit). And just as in electricity where a thicher wire not only carries more amps, but also has a lower resistance, a larger coolant tube will offer less resistance to flow.
And as I kind of hinted towards, but didn't say as clearly as I meant to in my original post - I don't think it'll make much difference in one of our systems which size you go with, but if you don't have the tubing yet you may as well go with 1/2" and get every little bit of advantage you can get out of it.
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