Support for units with two brushless motors?

[RobM]

I've been enjoying my afterburner thermostat for a little over a year now and it's been a lifesaver ( and energy saver) in use for basement heating duty as an alternative to electric heat.  My only issue with the setup has nothing to do with the thermostat but is due to the fact that so much heat gets wasted out of the exhaust pipe. I had been toying with some ideas to fix that when I came across some newer units that had dual brushless motors.
Essentially this allows for separate control of the combustion and blower fan speeds.  By all accounts this helps enormously with efficiency (reports are that it reduces exhaust temperatures by over 200° ) and also allows greater blower speeds for better circulation.
Any chance for afterburner to support the setup anytime in the future with software updates and or Hardware if necessary?

[afterburner]

No. The Afterburner is not an ECU.

The ECU is what controls the motor even in a standard unit.
You would need an appropriate ECU and proper coding of that to achieve anything, including matched fan speeds to mimic a normal heater.
Then the whole hoary world of correct tuning of air/fuel ratios also would be a big factor towards success.