I would have said Hive is not the thermostat for that set up. So either change set up, or use some thing like EPH.
Often the pump is wired to over run so that any heat in the boiler is still pumped to the radiators or hot water cylinder.
Once the motorised valve closes the pump can do what it likes, but no water will circulate. So where the valves and pump is built into boiler yes a run on can cool the boiler without it going out of the flue, but all the pump will do where the valves are outside the boiler is lift the by-pass valve.
It does vary boiler to boiler, I have been advised with my boiler with no run on to fit a motorised valve on the DHW will put a strain on the boiler, this was where the three port valve and Y plan was so good, as default was DHW. I am however using a C plan.
The S plan was considered in many ways better than Y plan because it could have many zones, but the TRV in real terms made the S plan redundant, I have in this house 9 motorised TRV heads so 8 of my rooms are independent of each other, (two radiators in one room). The remaining 6 rooms one is a shower 3 are toilets so don't want them to turn off, but 4 rooms form a flat so I can turn off whole of flat using a motorised valve, which is in turn controlled by independent wall thermostat.
If your house is split like mine so for weeks one set of rooms is not used, then motorised valves are good, but if like the main part of my house you have rooms used at different times then they need independent control which Hive is designed to do with TRV heads not motorised valves.
So likely you want both zones controlled by same wall thermostat, there is likely no point being able to turn off down stairs or up stairs as the TRV heads do that room by room rather than floor by floor, so my wife can have craft room heated which is up stairs and still not heat bedrooms.
If we think of zones being a collection of rooms then one room in each zone needs a Hive TRV head, so for example if three rooms used as bedrooms, only the coolest one needs a Hive TRV head, other two can have a cheap programmable TRV head. But as the use each room is put to varies over the years, it is easy to swap which radiators have the Hive TRV and which have cheap TRV heads, no wiring simply screw on/off.
In the main no point is zone valves for collection of rooms, as the TRV heads do a better job.
