That is an awesome setup. Way to take advantage of the renovation period to find a very efficient way to heat the home. It's  a weird problem running into the HVAC and the miners fighting each other for a stable temperature. I've never delved to deeply into the automation side or smart home systems. I would think though that you should be able to remove the home thermostat entirely from the equation for fan control. Have one upstairs that sends the heating/cooling demand to the fan circuits, and the main one is there to handle the house HVAC only. Maybe a different brand as you mention you think Ecobee is the issue there.