Your expeditionary fleet has waged their own campaign for a while, and forged their own alliances and grudges. What are they?
You get to choose up to 3 Sworn Brothers. But to balance it out, for every Sworn Brother you pick you also have to designate 1 By His Command and 2 Distrusted Allies. Everyone else is Fellow Warriors.
Custodes, Assassins and Daemons are Agents, and thus their ally level is based on Allegiance, rather than faction.
That's 19 Factions: 17 legions (plus your own), Humans (SA & Militia) and Mechanicum.