I had trouble with my heating system and got a good long talk with the HVAC pro.

I think variable output heating/cooling has one interesting capability - it can adjust to things you've adjusted. For example, a one or two-stage heating system has trouble if you close heating vents in some rooms. It might overheat if too many are closed for example. With a variable-output system, it can support this. further with variable dampers it can support zoned heating and cooling. You can give the places that need it less or more airflow and have a more comfortable house without waste.

after seeing things like heatermeter (pid controlled smoker controller based on the raspberry pi), I wonder why this kind of convenient and efficient control isn't more common.