So let's me get this straight, Naoto' strory is something like this:
In the Blazblue world, a Naoto certainly existed in the past, HOWEVER, he died at the hand of Clavis.
HOWEVER, there's an alternate reality that he survived and that world is Bloodedge Exp.
But now, reality is breaking down, every alternate world has disappeared, leaving Blazblue world the only timeline still standing (for now).
HOWEVER, Raquel manage to save Naoto from being erased along with his timeline by booting him out of the Bloodedge Exp world and place him into the Blazblue world, passing him off as "Ragna", which slowly overwriting the real Ragna existence because clearly the world hasn't shit on Ragna enough as it is.
So basically, when they say that the Blazblue world is the "origin" of Naoto's world is doesn't mean that Blazblue happened before Bloodedge Exp. It just mean that the Blazblue world is like a big tree trunk and every other worlds, including Bloodedge Exp, are the small branches.
Did I got that right?