Steve,
The menus for "Extraction Options," "Setup Options," "Output Options" and "Mode Options" do have the right hand menu as you describe (see picture below), but whatever I specify in one menu option (say Output Options, for example) will automatically show up in the other options also. This is why I was wondering what the distinction was.
You'll also note in my picture that no matter what menu option I pick, the "dialogue" box just says "Setup Options" rather than the specific option I'm picking (unlike yours, which says "Model Options").
Furthermore, I don't have a Model option, but a Mode option. Maybe this is a difference between v2014 and v2012 ??
Would like to know if someone out there with v2012 has this same situation.