Dark Beginnings, it stated everything Shadow the Hedgehog started from a Doom's Eye, that he was built from it's DNA, and that the Time Eater began functioning before the events, as GUN had records, and that Doom's Eye which is just a terminal started moving; the Doom's Eye being active means this is why Doom was aware of the future from whatever time period he was drawn from. Given Shadow's DNA was branched from a Doom's Eye (with whatever changes Gerald made), that means he at least contains whats needed to be a terminal for Doom, plus the fact hes capable of autonomous actions. To me, this all implied that Doom was trying to maximize the Black Arms DNA in him to make his body, which still exists in the future, capable of sustaining Black Doom's existence, and download himself into it. Not sure how well physical integration would do when the time distortion fades.. kinda seems like it would loose a ton of mass instantly, and if it survives loosing all that it would still just be the mental integration