As far as I know, The Order, The Nomads, the Nomad-infested navies and 4 factions from the SP campaign, are hard-coded (that is, not in the ini-files)
not to show up.
I've created a new faction, also called The Order, with the nickname co_or_grp, and gave it a very high rep end empathy values with the real order (in Empathy.ini and Initialworld.ini), so that the player's rep with this faction will always be the same as his rep with The Order.
Now, a faction only shows up after the player has had contact with it. so "The Order" only shows up after the player has met their evil twin. You can do this by giving a bartender the affiliation of the fake-order. I guess you can also give a base the reputation of the fake-order. Other NPC's at bases, or ships, are less preferable as you will have an audio file missing (Instead of "I work for The Order" and "This is Order" you'll hear "I work for ---" and "This is ---"
.
But maybe modding
Knowledgemap.ini does provide an easy solution -- please let us know!