Nx's mod.ini is the way it's supposed to be set up. The high-poly Faustus contained in the FSPort mediaVPs is supposed to have the additional dockpoints, and it did the last time I checked. Has that changed?
Nx, you can remove the primarylist line for the duration of that particular mission, and then add it back in once the mission is complete.
EDIT: And it should go without saying, but you should also make sure you don't have any loose model files or VPs hanging around.