Again, we don't know what the story will be. All we know for a fact is that reading Secret Origin
helped David Goyer "to grasp how lonely Clark must have been when he was growing up. And what a sacrifice Clark must continually make by being Superman." In other words, it informs his approach to the characterization
of Superman. We have no information on whether the actual plot
of Goyer's script will be based on Secret Origin
; that's pure speculation.