^Well, that's a given. The only IDW Trek comics to take place in the novel continuity are those written by novelists like KRAD or Peter David. Or that were retroactively embraced by the novels, as with Blood Will Tell and Alien Spotlight: Andor. Many of IDW's miniseries aren't even in continuity with each other; for instance, D. C. Fontana's The Enterprise Experiment envisions the late 5-year-mission era and the fate of the Klingon-Romulan alliance differently than John Byrne's comics do.
I'm not saying I'm surprised that Braga's comic is out of continuity with the novels. Of course it would be -- not only is he a busy TV producer who's probably never read the novels, but he's much higher in the Trek hierarchy than us lowly tie-in authors, so nobody would expect or ask him to follow the novelists' lead. I'm just noting the coincidence of how close in time these two radically different takes on the Borg's future happen to begin.
I wish some of you ''peons'' were in chrage of VOY, not him.