Your overthinking it. As long as you set the reference to zero when the throttle is closed, then your fine. That's all you are doing when you do a reset is setting a reference of zero with the blade closed. After that, setting the 5.5% is only a starting point so it will idle. At that point adjust your idle where you like it and ignore the position numbers as they no longer are in reference to the reset, just showing how far open the blade is. It is no different than opening the throttle and watching the throttle position change.
Matt