Now, I'm being told by my boat engine supplier to connect the inlet hose to
my new calorifier by drilling and tapping a plate on the engine heat
exchanger. This point is clearly on the secondary side of the fresh water
cooling circuit ie. "after" the thermostat. This doesn't seem correct to me

After the thermostat is open and coolant is flowing, the coolant temperature
will be roughly the same on either side of the thermostat. In fact, if the
coolant has to flow any distance from the thermostat to the heat exchanger, it
will pick up even more heat along the way. It's the heat exchanger, no the
thermostat, that changes the temperature of the coolant.

If you take the coolant out before the thermostat, you could prolong the amount
of time required for the engine to warm up.
You'd get a lot less heat a little quicker, but create more air pollution and
accelerate the wear-out of the engine as a result.