Don't worry about being critical. I do tend to overthink things. Glad to hear you haven't had any defrosting problems. I havn't driven mine in really cold temps yet so I didn't know what it would do.
Since you have the multiple heating zones in your system it makes sense for the hydronic 10 to run continuously and to control the heat with the circulation pumps. I think this is how a house with a central boiler and zone heat is set up. Since I will have only one zone. I would like to set it up so that the hydronic 10 could shut off and start up to maintain a preset temp.
I have the 7 day timer as well. I was reading in the hydronic 10 manual that the timer sends a 12v or 24v signal to the controller on the heater to turn it on. The burner will remain on until the signal is turned off. When the signal turns off then the burner shuts off and the heater goes into cool down. There is an option for a simple push pull switch to turn the heater on and off in the wiring diagram. I think this could be replaced by a thermostat. I agree that I wouldn't want to short cycle the heater by having it constantly turning on and off. I think this would lead to soot build up in the combustion chamber. I think that by wiring a timing relay between the thermostat and the controller the burner could be ran for a preset minimum amount of time.
My water heater and water tanks will be mounted inside the bus to avoid freezing.