I am not able to do what you suggest using the configuration tool. Using the Config tool, I can set Ext 1 heater and sensor as you suggest, but these settings are not present if the mixing extruder flag is checked. The Extruder 1 settings that remain after the mix check box is set are only the settings of the extruder stepper motor and the three check boxes (ending with the one about motor mirroring). All other extruder settings are not present.
I can do as you suggest if I modify the configuration.h file, if that is what you intended.
For starters, I am less interested in setting up a mixing setup than a switching setup (a shared extruder?). What I was hoping to setup is essentially a dual extruder using a 2-to-1 nozzle and changing extruders with either with the TOOL CHANGE g code command, or let Repetier Host operate as a normal dual extruder with a two color model (and let the color transition happen as it will in the 2-to-1 nozzle).
It looks like I can take a configuration.h file that is proven to work as a dual extruder and make minor changes as suggested above to achieve either a mixing setup or a shared extruder. Maybe it is that simple, but I have no clue what the firmware actually does with either of these check boxes.
I don't believe that I will be the only person that will be trying to understand this. I would be more than happy to help expand the documentation if there is anything I can do.