I've been programming computers since 1974. (That was FORTRAN-IV on punch cards!)
Depending on how powerful your Rule system is (can it calculate the time between two events and act or not act on that time difference?), I can program to distinguish an event coming from the thermostat that was done manually from one sent by the controller and then immediately echoed back.
Or, perhaps simpler, make the Rule smart enough not to forward to the controller an event coming from the thermostat that doesn't change the set point temperature already set in the controller, to avoid the loop caused by the echo. The Rule would have to be able to save state between calls, or be able to query the controller to find the current temperature. It would also need to know about time, so that it didn't act on every button press immediately but waited until things were stable.
I don't know how powerful your Rule system is yet.
Or, maybe I can use the device event log from MakerAPI and issue commands from my Linux system to HE that way. But the Thermostat Controller events are missing. The MakerAPI app logs events from my thermostat, energy meter, and temperature sensor, but even though I've selected the controller I get nothing in the MakerAPI log. I suppose I can work around that by explicitly querying the controller via MakerAPI, since that seems to work. I'll have to read up on what's possible. (Why don't I see Thermostat Controller events logged with MakerAPI?)
Or, maybe I should look into getting my Nortek USB Controller working under Linux. If I can see events through that, I know I can write a program to do what I want. (But maybe Z-Wave devices can only be seen/managed from one place, so that if the device is "attached" to the HE, it won't be visible to the Nortek?)
This is all new to me. What fun!