I actually see it in a linear way.
The thing is that even though he uses flashbacks on "Following" and "Memento" he relays on chronological distortion to tell the story on these movies, not the flashbacks.
On "The prestige" he is always telling the same linear story using long flashbacks to tell the story and then back, like Borden reading Anger's diary in which he is reading Borden's diary, etc...