Gallic Junkers being privateers for the Gallic Crown was not retconned out.
In fact, it was retconned in for 4.87. Beforehand they were a faction without too much direction.
As for the current relation between them and the Sirian Junkers, I'd say it should be (in rephack terminology) either unfriendly -.3 or no dock -.55.
Their initial lore tie between them and the Sirian Junkers is ... probably inaccurate. And their current situation, nebulous. I think the current stance is that there was some link waaaay back when, but it dissolved shortly after it became a thing and they've disliked each other since.
Whether or not you agree with that, Igiss' original explanation, or believe there must've been no connection whatsoever, having an unfriendly diplomatic stance is still probably the best bet.
The Sirian Junkers have openly opposed the Gallic Crown, whereas the Gallic Junkers work for them like mercenaries. While they share enemies (Hogosha, Unione Corse) and friends (Outcasts), there are many differences in their relations beyond the GRN/GRP. Gallic Junkers aren't (or shouldn't be, if they indeed are) illegal in Kusari, because they work for Gallia. They are also hostile with Liberty, Bretonia, the Colonial Republic, Maquis, and Council. Their namesake counterparts are the opposite on all of those.
I don't know if this helps with your idea, but with luck this clears things up
"You see what your knowledge tells you you're seeing. ... how, what you think the universe is, and how you react to that in everything you do, depends on what you know. And when that knowledge changes, for you, the universe changes. And that is as true for the whole of society as that is for the individual. We all are what we know, today. What we knew yesterday, was different; and so were we."
- James Burke, The Day the Universe Changed (1985)
