I find Rogue Trader slightly paradoxical. On the one hand, they have nigh-infinite power, within their sphere, and access to the best of everything, but on the other hand they write much of the material so that it can be baby's first adventure, and so many "planned" events are not to hard, once you get some gear and XP under you. I say this because I think, from the book's perspective, they want your players to have to act out building some of that spy network, or finding those rare-in-the-Expanse Space Marines, and prostrate yourself before them, hoping to become friends. While the building project you describe would be neat (systems like Stars of Inequity might even benefit if you had a more real list of "things the Dynasty has just sitting around"), the book often takes your Dynasty as brand new, meaning you DON'T have those things, and need to use good role-playing to get them, rather than picking them off the list.Oath-Bound to the Angels of Death was a cool Ascension talent, but not one you should just get to spend XP on; prove to me that you have earned the respect of the Astartes! That sort of thing.
Also, Rogue Traders lose so much power inside the Imperium, I imagine many of them, with their Ork Mekboys, Kroot mercenaries, and grav sails just avoid the whole place as much as they can, maybe going to Scintilla or the Lathes when ABSOLUTELY necessary.
I might be a fan of another book of places, with unique treasures, some awesome salvage or trade opportunities, and plot hooks aplenty. A handful of off-things in Lure of the Expanse can be more intriguing than it's end, and I like how Hostile Acquisitions and the Koronus Bestiary both draw from its unique places, and add extra cool options to these already options of the Dread Pearl quest. Some more places, be they lost planets, ghostly stations, hulks, or what have you, and the cool information, artifacts, and monsters you might find could be awesome. Looting a ship of the Astrarium AND a ship's unit of enhanced boarding-repelling Murder Servitors would be a nice day, especially if it was on the way to a world where some cool weapon was said to have been lost (ship or personal, I don't care). I know I could make these things up, but sometimes I'm just short on creative thinking.