Well the thing is, you can't have the Nomad faction public because then you'll see nomads everywhere attacking everything. And that would get old pretty fast. Unless of course you give them a zone of influence - say the Omicrons. That would tone down the mayhem. But then you'd also have the Iseijin and Das Wilde in Kusari, Sigmas Rheinland and Omegas.
As for the SCRA, HF, RoS and CR - they should all be open factions since they are not terrorist nor Sirius wide factions. But you can't reason with the leaders of the mentioned factions, because they will claim that these factions belong to them, and it would ruin their little world. While that may work for a faction like the IND, which only has custom ID (yet), no ships or bases, it doesn't work for the above factions because they do have ships and bases. And it's only fair to the playerbase to be able to use them without having to join a player faction.
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Mephistoles