It doesn't make sense to me to optimize for equal load (runtime?) between zones. The point is to make both zones comfortable for humans. If you use both floors, IMO the temp should be set the same in each zone - whatever is most comfortable for you/your family.
In my 2-story house with separate HVAC units & thermostats, I only use the main floor (with MBR), so in winter I set the 2nd floor cooler and in summer I set it higher. I do that because I'm not up there much and don't care about comfort, yet I don't want to turn it off altogether, which would cause the main floor unit to work much harder.
Shouldn’t the goal be to optimize for warmth equilibrium and efficiency? In turn it is the most efficient load for the furnace and also for comfort. If I were to optimize warmth for the 1st floor ignoring the 2nd floor, the heat loss towards the 2nd floor will still occur due to physics, and now the 1st floor zone will be working much harder because it’s really warming both floors now. What should the setting be for the 2nd floor in order to make it a blanket minimizing the upward travel of heat from the 1st floor?
I don't know why you want to balance your furnace load between the two zones, but anyway if you're comfortable, you can do it by raising the upstairs temperature. But to optimize for comfort, set both thermostats the same, and let the lower floor do more work. If you're heating the same amount of air to the same average temperature, I don't see why the overall efficiency would be different.
In my 2-story house with separate HVAC units & thermostats, I only use the main floor (with MBR), so in winter I set the 2nd floor cooler and in summer I set it higher. I do that because I'm not up there much and don't care about comfort, yet I don't want to turn it off altogether, which would cause the main floor unit to work much harder.