They run the junker tag and ID because it more closely suits them than anything else available in-game right now.
Anyways... I would strongly suggest that if you want to "take control" of any part of bretonia, you do it with the systems that are 'blank'.
Example: There's a system linked to dublin called the Chester system. There is nothing there, save for a single wreck, an 'unknown' planet, and a star (or maybe a few stars, not entirely sure). That system isnt being used for anything, and once your faction is established you could 'buy' the system from the admins and get one of the system developers to put a junker base or two into that system, and claim it as your own. It's still part of bretonia, but would be governed by your faction (the junkers).
The problem with trying to claim the space around trafalgar is the same problem junkers in new york and new berlin have with our stations. Rochester is in new york, but that space is still technically owned by the liberty government even if our station is there. Likewise with kreuzberg base in new berlin - we dont own the territory, only the station.
Now, Personally I say that 2000 meters around every junker station is part of that station's 'airspace' and belongs to it. We make rules in that small area, but many of the houses dont recognize those rules, and still claim to own that space - that your station is just a 'guest' in that area.
So really, you can never own any part of a major house system... you'll have to claim bordersystems or areas that are currently unowned.