So, you are playing a Navigator in your game; an important soul who comes from a Navis Nobilite House that is part of an organization almost as powerful as any other group in the Imperium. No matter who you are, if you want to go practically anywhere in the galaxy, you need a Navigator's skills and services to manage the voyage. This puts the Houses of the Navis Nobilite in a very good position to accumulate money, power, and connections, the same as the AdMech, the Ecclesiarchy, etc. That being said, would your House possibly have a Profit Factor, or Influence score, and could you possibly acquire things through it, rather than through your RT's Dynasty? I'm not trying to find a way around low group PF, but I am wondering what sort of mechanical advantages said navigator might have of being from their House, and showing how the success of one, the House or the Navigator, could be shown to benefit the other? It just sort of seems weird with fully developed organizations out there, like the AdMech and the NN, that such characters as hails from them would cut off ties and ONLY get stuff/benefit from their Rogue Trader business partners.
I do, of course, see that AdMech and NN characters can get Peer (though the Navigators never get it for their own organization on their path?), but am not sure what you would use it for, as a Navigator. You could buy their services, but you already PROVIDE that service, yourself.