I believe that the main reason that unofficial factions (a tagged, minimally organized group) are bound by most of the rules that official factions have to follow is mostly for that reason alone. Official factions are by ID and lore to follow a path, and they are encouraged to promote and represent the npc factions they are affiliated.
A hypothetical example: If suddenly you find the Bretonian Armed Forces facing a tagged group consisting of BMM ID ship in line with pirate ID ships flying Corsair tech, it is a possible scenario for players, but an impossible scenario for BAF as a player faction and a lore established entity. How would they deal with it? Would they consider the BMM Id as the guideline to establish their position with this absurd faction, which should be Bretonian citizens then? Would they consider the Pirate Id, even though they would have to outlaw several bretonian accomplices, for crimes they may have or have not been involved? What about the Corsair ships, does it make it a Corsair backed group? Are these corsairs then?
This is the main reason why I believe the "one tag, one Id" rule is in effect for all factions. You could have a majority of freelancers, or pirates, or miners in a group, but the first time a non-generic ID vessel comes into play, it binds everyone perspective of that faction to that faction ID.
I say that there are a few plausible scenarios that can work within the current rules, that may provide a mixed shipline set, within reason:
- A full generic ID faction (freelancers, pirates, whatever), roleplaying their development with the factions and houses, and acquiring their (faction) ships with the producers. Being a freelancer or a pirate does not entitle you to a dragon gunboat or similar, just because you can buy it from their base.
- A faction x group, using that faction ships and roleplay, but developing a splinter faction from the original lore, getting deals with other factions for ship and relationships. Eventually such group would need to get it's own ID to get free from the lore and restrictions of the faction ID they were based on, thus becoming a new official faction of this new hybrid group. In this case, generic ID's in the group are still subordinated to the main non-generic Id.
- flying untagged, an unknown but effective group of collaborating individuals. In here, individual ID rules apply, so even if you find two pirates flying a corsair gb and an outcast bomber respectively, other groups could still respond to the situation as an encounter of pirate 1 and pirate 2, and proceed accordingly.
This is what happens with indie OC supported by rogues in Liberty. They work together, but factions can act considering the OC and the rogues as separate entities acting together on that occasion alone.
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If I have understood correctly the situation on the GNG case, is that their flaw was that they put the generic Pirate Id above any non-generic (Rogue?) Id's their members might have used. those rogues members wouldn't accept to shoot other rogues on behalf of a indie pirate leader in any case, if they were still using a rogue ID.
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TL,DR - With current rules, and for the sake of RP sanity, there cannot be a faction where a non-generic ID is subordinated to a generic one. Once a faction ID is used by a group, the best that group can do is to not go against such ID lore and rules.