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.

For that matter, I'm really unclear as to how to acquire more Navigators! Inevitably, a Rogue Trader will start to accumulate ships, and those ships will need to be flown…

I'd run it as a potential Endeavour component. The Navigator could potentially convince his House to invest in projects, opening up an avenue of wealth that would otherwise be very difficult to break into.

As to acquiring more Navigators, the way I see it, once the word goes out that a Rogue Trader is after another Navigator the Houses will be competing for the contract with each other - even if they pretend not to be on the public face of it

I know that in the story I am working on, the Silver Ravens (House Korvallus) are supplied entirely by Navigator House Volaris, as far as Navigators go. When Lord Korvallus, or one of his empowered underlings (the old man isn't quite so spry as he once was) acquire a new vessel, and need a Navigator, they contact House Volaris, and Novator Daedalus Volaris arranges for one. I think many RTs have a contract of sorts with specific Houses, drawing most of what they need from one, when possible; this would add a layer of partnership to the arrangement, with the Dynasty showing loyalty, and garnering quality service, while the Navigator House garners wealth and stellar information, increasing their prestige, and such, as well as that of their patron. That way, both have a vested interest in seeing that the other succeeds. A Dynasty like Winterscale's, of course, might tax the output capabilities of any House, but he's an exception, I would think. House Korvallus is reasonably small, despite its successes over the last century, and so one decent Nav. House can supply the Silver Raven fleet with all it needs, and still have a few for the AdMech ships that the Volaris House is allied with (techno-marvel or not, I presume Mechanicus ships still use Navigators, rather than the weird engines).

The biggest reason I see that those characters cant use their respective organization's effective profit factor is that unlike the rogue trader, they are not the heads of thier organization. While their organizations may be big and powerful, the characters (early on at least) don't have any major pull with them.

I don't really see the navigator houses as being like RT dynasties, but more like mafia families and your character is not the Don

Simply put, a Navigator recieves mechanical benefit from the house he is from as per character creation in the book (pers, mutations, powers etc) and is afforded the status of Noble for all intents and purposes. They may not be in charge of the ship, but the ship's Captain is a peer and not a superior to them and so a great deal of respect is afforded.

One option is for a small bonus (5-10%) when making acquisition checks for items specifically manufactured by the PCs faction (Bionics for Explorators for example) or giving a small achievement point bonus for endeavors that directly involve that faction. Obviously this will need to be under the control of the GM but it is logical as PCs are bound to have contacts and inside information that will be useful.