And, of course, Braga (and RDM) referenced an alternate universe in "All Good Things..." where the Borg had done the same.I think it's more of a happy coincidence. After all, the same idea (the Borg eventually assimilating the galaxy) was used slightly differently in IDW's Alien Spotlight: Borg.
There's no such reference in AGT. I think you're thinking of Parallels (solely written by Braga) in which we do get a glimpse of a universe where the Federation has been overrun by the Borg.