Both Fury and Miles were from Ultimate, and are the only two things that made it out of that world's cancellation I believe.

The one in the main continuity debuted literally right around the Avengers movie, and its literally "OG Nick Fury fucked some black agent, this unrelated previous character's real name is literally Nick Fury Jr. and he also shaves his head and lost an eye." Which they then made Original Fury stop being used almost entirely and let this one take on basically everything Fury would normally do.

Miles being just Spiderman also isn't something they pulled out of nowhere originally, but its a bit different now that Spiderman isn't dead and circumstances aren't the same. No different than the gap between "in this universe he was always Sam Jackson" and "his identical but black son we never mentioned for 60+ years will take over his entire existence."