That's an interesting wrinkle...but probably as forgotten as that time Barbara Gordon was Jim Gordon's "niece."
I'd probably have to re-read Johns' second run again (not that I have any major desire to re-read Rebirth) but I feel like there was a little more to it then that (and on the issue of being neglectful and distant, the second arc was him trying to grow out of that).
Of course it's all kind of a moot point once Flashpoint hit...