I still suspect Craft's people are human of Earth origin.
Yes, Craft is explicitly human, but there's no rule that says all humans have to be in the Federation. We already know of human populations that aren't, like the colonies in "Up the Long Ladder" and "The Masterpiece Society," for example. And as those of us in the United States must know if we've ever taken a history class, it is possible for a colony to become independent from, and even go to war with, its founding nation.
Oh boy, if we start decanonizing episodes that actually appeared on TV, that will open up a can of worms.
Voyager's own producers disavowed "Threshold" as an apocryphal story over 20 years ago. There have been other stories over the decades that have been implicitly treated as apocryphal and contradicted by subsequent canon, like "The Alternative Factor" with its bizarre, warped version of how antimatter works, or ST V with its ridiculously short trip to the center of the galaxy. And there are borderline cases, like DS9 ignoring or changing virtually everything "The Host" established about the Trill beyond the basic idea of their symbiotic nature. "Canon" has never, ever, ever been a uniform, consistent thing in
Star Trek; fans have just gotten very good at denial and rationalization in order to buy into the fantasy that it fits together.
"Canon" just means the overall body of stories by the creators or owners of a franchise, as opposed to tie-ins or fanfiction. Lots of canons ignore or overwrite parts of themselves, like how Marvel Comics constantly rewrites its timescale to pretend that stories from the 1960s happened only 10-12 years before the present, or how
Dallas retconned a whole season as a dream. A canon is an overall whole that pretends to represent a consistent reality, but since it is just pretending, that means individual details don't always remain consistent in actual practice. Canon is the whole, not the parts.