This is mostly because the Dark Heresy was published originally by a different company than Rogue Trader was. When Rogue Trade came round FFG was able to do things the way the envisioned it. It also simplified it was well (thank god for universal weapon trainings)
So really it is mostly caused by differing ideas of what they thought the system should run like.
I myself am interested in getting the DW book simply because I have been running a SM campaign and the players are loving it. I find the most interesting part about it so far is that the other person who GMs a DH campaign when I'm not running is all kinds of run and gun, ignore the inquisitorial/RP aspect, and we are playing, scum, psyker, guardsman, assassin. Our conversation amount has been very limited and we have basically been dragged along the whole time being told what to do by a higher up, who isn't even a member of the imperium.
Me running my SM campaign has been about 80% RP and then the other 20% is actual combat. I haven't had a single complaint any session and they tell me they can't wait to continue, the other guy...I think we stopped his. I feel like I messed up or something by doing it this way, and that I should be playing run n' gun (which everyone said we should do) and now we are spending 6 hour sessions talking in character to NPC inquisitors and solving an issue on a planet, that should really just be blown to hell w/bolter fire...they are fricken reasonable marines at this point to me