Further to that, there has been no single "keeper of the vision" over the course of franchise history, so things are bound to get a new take on them or some things just completely forgotten about. Damon Fairclough did an excellent job of keeping a consistent lineage on the originals and up to 'Fusion, but some of the content for 'Fusion was conjured up by the development team and it was clearly at odds with Damon's stuff. Then I came along after that and, for about 3.5 years through Pure, Pulse and HD it was at least the one person making sure everything was in keeping with the universe.
I was long gone by the time 2048 came out and I considered it to be a total reboot because it had taken things from the games set later that were a paradox in the original timeline. Once pick up absorbing and barrel rolls were cropping up 150 years ahead of schedule I figured that the development team had a fresh take on how it all evolved. I figured we'd see a new timeline progression on PS3 or PS4 sequels to 2048 that ignored the original timeline entirely, but as we know that wasn't to be.
So here we are - we've got a mix of old and new ideas in the Omega Collection that don't fit as seamlessly as we'd like.
I did write a much larger reply to this going over the transition of the back story for 'Fusion > WipEout Pure > WipEout Pulse, and how certain things came about but decided it was a bit lengthy. I'll stick it up as a blog/feature post if anyone is interested.