The novels aren't canon, but they're part of a bewilderingly intricate continuity which began in 1996 (with ties to novels further back in the 80's) and runs parallel to the canon Trek 'verse. And of course bits and pieces have worked their way into canon over the years (Uhura and Sulu's first names, the names of Kirk's parents, lots of Vulcan lore/katra stuff, the Vanguard station design etc.)
That in the novelverse they armed the Borg with time travel is somewhat silly, IMO, but it was an attempt to explain why the Borg didn't just keep trying the time travel thing until they succeeded.
Back on topic, I figured the Sphere Builders were native to the 22nd century. But existing in another dimension (or whatever it was) and having the ability to examine possible future timelines opens all kinds of doors for future iterations of them to lend a hand whenever necessary. We know from "Carpenter Steet" that they or future iterations of themselves have time travel abilities enough to be a threat to Daniels' people.
I liked that they were kept mysterious, that they were all female and had super powers (giving the impression they were witches). It's just a bit of a shame that they reused the protohumanoid (TNG: "The Chase")/Founder makeup again.