I have never used these controllers before so the following is just a guess.
I would say the controller giving an error when the throttle is below a few percent could be correct behaviour.
This could be the low pedal lockout to prevent start up if the accelerator cable has broken or become disconnected.
When you put the throttle control in the car the pedal would hold the throttle at something above zero with foot off.
I would imagine there would be a high pedal lockout as well which would bring up an error at 100% throttle control travel. Full throttle from the pedal (foot flat to the floor) would likely only give 95% of throttle control travel. Anything higher would be recognised as a possible return spring break and present an error.
I imagine that is why there is a calibration sequence so the controller can find where the zero pedal travel and full pedal travel appear in the available throttle control travel.
Once again this is just a guess but it makes sense to me.