You are correct about the 2 thermostat "zones. "The "water tank" heat exchanger is in series with zone 2 (the bedroom.) It is just a separate input and control for its fan, that turns on the pump that services zone 2.
If you look at the diagram above, you will see that the "water tank" thermostat is input 4. (inputs being numbered 1 thru 5 to the left of the zone 1 and 2 pump listings.) WRV doesn't' use the separate bathroom and bedroom inputs and you will see that pump 2 is controlled by inputs 2,3 and 4, while each input controls its own fan.
2007 Limited SE 40fdts
Las Vegas, NV