I'm not sure what you're asking here. I think the Auto Configure Extruders options are used on multi-extruder printers to automatically setup the extruders to do either single or dual extrusion. For example, if printing with only the right extruder, it would disable heating of the left extruder and customize the starting sequence that is used since you only have one extruder to deal with. For a dual extruder configuration, it would heat both of them and have a special starting script for that too.
I'm not sure why you would want to disable that functionality. That's the main purpose of that option to begin with.