.... every fall I drain the HW tank and remove the freshwater gozinta and gozouta hoses, and use a M/M coupler to clamp them together so the pink antifreeze can run through the lines without affecting the HW heater tank. The little bit of water that might remain in the tank isn't a freeze issue because it's got room to expand. In Spring I re-attach the hoses to the HW heater tank after I chlorine-shock the fresh water system (which I do as part of my Spring commissioning, to kill anything that might be growing in the water lines).
Running the engine with the fresh water bypassed is not an issue. If I haul out late I might winterize the fresh water system before I haul out, just to protect the fittings.