Well, the last alignment was sometime in 1925 so I doubt they would have realigned this soon.
Ah, but this assumes the tales are completely true. Often they are peppered with deception and misdirection, or even so far as complete hallucinations and nightmares of days gone by. Frequently this is due to the madness of those involved. One does not truck with Cthulhu and retain all of one's sanity.
The madness also probably explains the rampantly inconsistent spelling of things... not to mention pronunciations.
In the novels, Hugh's faction reappears as allies of the Federation, and they capture and recycle borg technology (since they no longer assimilate people to get resources)
So, thats why.
The statement I quoted said a Borg faction, not a rogue Borg faction. And in reality, Hugh and his comrades were no longer "Borg", they were something else. "Former Borg" if anything. So why would the Borg faction itself be flying a captured Borg sphere?