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.
Well.. going from that, here's an idea
Craft's people on Alcor IV originated on Terralysium. It would explain their lack of obsession and knowledge with the Long Ago media. They never had any, and had largly become their own agrarian civilization by then. It supports the idea that when Discovery is parked in that stormy gas cloud, it is much further down the years.