There is no reason why a flashback story cannot be the main event in the flagship book: otherwise, Johns/Lee's Justice League wasn't the new52's flagship title when it was set five years back.
I was the one who mentioned that the flashback Batman story was probably going to pick up the Gates of Gotham/All-Star Western theme of Gotham as a sort of character, with the story shaped by architecture and geography. I'm standing by that and I'm interested. (Harper Row looks far more like a colossal dead-end to me, more of Snyder's revising the ideas of others and pretending it's new.)
I think the opposite. Snyder seems to have abandoned the secret history of Gotham idea. It's only a subplot for All-Star Western and barely that now they are moving onto the Steampunk Stormwatch. Harper is VERY likely to be the next Robin given how he got Becky Cloonan to do the one shot. He has since revealed on twitter that he has known about Damien's death since he started on Batman.