As far as I know, it shouldn't affect it, it doesn't care what's hooked up to the coaltrol.
Is just the standard fan on the stove or your larger furnace blower? Still should not matter.
There is no feedback from the fan, it just sends a signal to run faster or slower (on/off) depending on the temp requirements.
The only feedback is the Thermostat settings, based on the set temperature vs. room temp, it will vary the outputs (stoker, blowers, etc..)