Official factions are supposed to guide the NPC factions they represent as they develop, not move away from them. I think the whole proposition is useless for that reason.
To address more specific points, I think it makes perfect sense for Rogues to kick their competition from their bases, especially when they turn against their hosts more often than not. If you pirate in Liberty and you chose a Pirate ID instead of a Rogues ID, this specifically means you want to be a pirate that is not affiliated with the Liberty Rogues.
I hear the argument "this is freelancer, not factionlancer" so often, as if the statement proved something... The logic of that argument fails where Freelancer was designed to be a singleplayer game, you're a freelancer in a world of factions and diplomatic events. This doesn't work if every inhabitant of Sirius wants to be a freelancer. I might just suggest renaming the game to Discovery Factionlancer instead, because I'd much rather have roleplay based on the interactions between factions and their members, than a universe that consists of freelancers doing whatever they want.
