Yeah, Phantom NPCs serve more than one purpose. Firstly it gives Phantoms their NPC faction to use the tag of, which is really nice. Shows up nice ruby red on all my huds (Until I go out and slaughter things like Militaries, now they are nice and white on my GC:D).
Then the Phantom NPCs also allow factions on other servers to be terrorists in their own way. Instead of being the Liberty-specific Xenos Terrorists, or the Kusari Blood Dragons, each with its own unlawful enemies, you can be the Phantoms and be friendly to most unlawfuls, hostile to all lawfuls, and able to operate within RP, but not being restricted to certain areas of Sirius.
Its because of the second reason where there isn't a Helghan NPC faction, or an Asgard Warrior NPC faction. Its also for the second reason why the Coalition ID was created. One can now be hostile to EVERYONE except a select faction (likely Zoners) to dock at bases with.