There is nothing really in flashpoint that connects the two - the coda at the end could have existed all the time with the costumes simply redrawn and the two page spread drawn or redrawn for that purpose.
Exactly my feeling. If you aren't paying attention to the different costumes in those final five pages or so, you wouldn't realize that they were different at all, and I prefer to think that they take place in the DCU, not the DCnU.
For one thing, I think it's emotionally unfair to the audience for the finale to take place in an entirely new universe. The Bruce Wayne there is not a Bruce Wayne we would have an emotional connection with. He's "a" Bruce Wayne, obviously, but he's not "our" Bruce Wayne, the one that readers have been following for years. Giving a stranger the emotional closure that we get in the final pages of Flashpoint
is wholly unearned.