Everything after the original series (all the live action and CG stuff, Alien Force, Omniverse, etc) is actually in-universe fiction. As part of building the massive organization seen in Ben10K, Ben started licensing out his story, on the condition that certain details were changed (i.e. his parents portrayed entirely differently so that the real people could live in relative normalcy). He's too busy to keep a close eye on things, but every so often he checks in, hates what he sees, and yanks the license. He was okay with the Alien Force one, but it had poor ratings and his business managed convinced him to go with another reboot. The reason why the continuity is such a mess is that it's not allowed to be 100% true to history, and different licensors find different ways around that.
(And yes, that makes the episodes about authorized or unauthorized Ben10 shows or games on the shows a case of the creators getting all hip and meta.)