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Boat engine cooling systems are different from cars, usually there is a rubber (not metal) impeller pump and the coolant (your raw water) is forced to be in constant flow. The impeller blades would probably break off from the backpressure if the coolant couldn't flow. The system is set up so that there is always a flow from the pump--the only question is, where will that flow be directed. The thermostat is a diverter valve (a "Y" valve) rather than the simple open-close type in a car.
"First off, the thermostat has nothing to do with the exhaust water."
Sometimes it does. You'll get a trickle from the bypass circuit while the engine is cold, and then when the thermostat opens (often a "Y" valve on a raw water entire) the primary cooling lines allow more water to go through. Could just mean that the bypass lines are smaller, or more constricted.
In raw water systems 140F is normal, because around that point salts crystallize out of salt water and jam the cooling passages. A very bad thing. If you are operating a diesel in FRESH raw water, inland with no chance of running in salty water, you can usually put in a fresh water thermostat which can bring it up to 170F-190F, a normal range for closed heat exchanger systems and fresh water. And, a more powerful and economical operating range for engines in general. (Obviously, to the limits suggested by your engine maker.)
But in raw salt water, you can't run an engine that hot. The lines will plug up totally in short order.