Maybe you should be carefull what you do here.
The question that stands out, why would one want to change the phase angle of the controller in the first place, if auto detect resets these settings.
To know these things one must of change the settings to 60 degree phase angle and boot it up to find the settings have been reset to 120 degree.
There is sensorless mode to consider too and possibly the controller need the hall sensors to be operational for the auto detect to work.
Maybe some of the settings are for testing the phase of the newer contollers, possibly, where they have no motor installed and need to see how the controller phase angle times under a oscilloscope..
Or maybe the auto detect features came after the software settings were designed. Maybe GM engineers have been using the cable software for years and only recently opened it up to the customers.
The auto detect in this case is the software users best friend. There be bad things that can happen when setting the controller to do 60 deg on a 120 deg motor.
Unless we ask the engineer all these questions we can only guess the answers.