It may be a restriction of the control you have over your heat source but could you try a different approach? I'm in a similar situation to you - a newly built near-passive house with UFH in concrete on the ground floor and a more responsive system (overlay UFH under wooden floor) on upper floors.
Ours is controlled by the gas boiler manufacturers Weather Compensation controller.
The pumps run continuously (at a slow speed) during the heating period (4am to 10pm) with a very low flow temperature determined by the outdoor temperature (theres a heating curve - right now it's 11C outside and the concrete floors are running at 21C, the wooden floors at 22C. the air temperature in the first floor room I'm sitting in is 20C. From memory the flow temperatures increase to about 24C/28C when its around 3C outside).
Flow rate between rooms is controlled by the manifolds but using manual valves (ie it's was set on install and left) and there are no room stats. Because the floor temperatures are so low you don't get overheating (the delta between the room and floor drops so heat transfer becomes minimal) and the temperature is consistent between rooms.
The boiler modulates output to control the primary (higher) flow temperature (for the wooden floors) and there a mixing valve to blend down the lower floor temperature for the lower floors.