Mike,
Maybe it depends on the Aqua-Hot model (or coach model and year), but what your owner’s manual says is very similar to how our wet bay heat exchanger works, except ours is controlled by an adjustable remote bulb thermostat.
Basically, the wet bay heat exchanger works just like the any other zone when that zone is set to Furnace. The wet bay fan (and circulation pump #3) will run ANYTIME the wet bay thermostat is calling for heat, even if the Aqua-Hot is off and the boiler is cold (which is not a good thing).
So long as diesel and/or electric are selected, the boiler will attempt to maintain temperature. Interior thermostat settings have no effect on the wet bay heat exchanger or burner operation.
Anyway, that’s how our system works.
It would be pretty unhandy if the interior thermostat had to be set to Furnace to allow the burner to fire. If that was the case, you wouldn’t have any domestic hot water unless the thermostat was set to Furnace.
Aqua-Hot model: AHE-100-04S
-Scott