Let me start this by saying that I hope that I'm wrong. But, it doesn't seem like Rogue Trader is really a stand alone game. To be sure, it does have the complete 40k RPG rules set in the book and, in fact, there are several subtle differences from Dark Heresy on how the rules work. Yet there is a conspicuous lack of support for the line -- only 2 support products (GM screen and adventure book) published so far and the 3rd game in the 40k RPG line is scheduled for an August release. Given that, and the compatibility with Dark Heresy, it seems that Rogue Trader is more of a "side game" or a supplement for Dark Heresy.
What do you think?
He has to answer to people ultimately higher than himself. He has stated as such.