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Separate or not, Space Marines still fall under the authority of the Inquisition... at least on paper.
No one, save the Adeptus Custodes and the God-Emperor, Himself, is above the Inquisition's authority. No one. No where. No how. While, yes, many organizations are large enough/powerful enough to challenge the Inquisition on this point (which the Inquisition well knows), Imperial Law, and the Emperor's own decree, always stand on the side of the Inquisition when it comes to questions of authority. Those who resist this, resist the Word of the Emperor, and are heretics.
Deathwatch, the RPG, gets a bit more complicated than just a simple ret-con, because it deals with a specific sector of space and a specific collection of Deathwatch forces. Yes, they have Watch-Stations scattered all over the Jericho Reach... many of which are abandoned or manned by a single Marine. One such Marine, poor bastard, has been waiting 40 years for his replacement to arrive!
There's also, given that this is tied into the Dark Heresy RPG, a cryptic prophecy circulating around the Jericho Reach that the ongoing war of the Imperium vs Chaos, Tau, Orks and Tyranids in the area is a prelude to something much, much worse... and only the Deathwatch will have a chance to stop it. This is why they sorta-kinda give the Inquisition the brush-off... they feel they have a higher calling in the region. Of course, they don't entirely tell the Inquisition to go feth themselves (they are still the Chamber Militant of the Ordo Xenos), they just operate with a bit more autonomy in this region, because they cannot risk committing all of their available forces to an Inquisitorial purge elsewhere when they have enough problems here to deal with. The Inquisition knows this, as well, and believe it may be tied into the Tenebrae Heresy, and so let the DW go about their business, calling in the occasional Kill-Team when they really need it.
Last but not least... it's a stand-alone RPG, but is written in such a way that you could include a DW character with a DH party, aboard a ship from the RT RPG, or any combination of the three. So, yeah, given that the Space Marines are GW's poster-children, their game is going to be a bit OTT in some respects because, well, you're getting to play a Space Marine!
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