Justice League Crisis On Two Earths/WMG

Owlman didn't turn off the bomb because, in another universe, he chose to turn it off.
It's the All the Myriad Ways rule.
 * Like he said before he died, "it doesn't matter."

Owlman was wrong about his theory of the multiverse.
Otherwise, there would have been an infinite number of universes in which he succeeded in destroying the multiverse, which is impossible because there are not an infinite number of multiverses. Second: He wasn't the only Villian to attempt this destruction. In Turtles Forever Shredder came up with same idea, and since Batman And Turtles met before... So there. Third: By not shutting bomb off he remained within boundaries of Multiverse. If he would've stopped the bomb, and picked up the remote, he would've succeded. But he didn't and thus made a choice that sprang another world where he died of hypotermia. But yeah... It doesn't matter.
 * Unless there are.
 * If he failed in even one universe there would still be an Earth Prime, and he did so there is. And as Word of God states, even if he had succeeded there would still be another Earth Prime where he failed. The Multiverse would be pretty brittle otherwise.
 * Which is why he should've sent just the bomb to Earth Prime. No sentient life, no free will, no divergence as to whether or not the bomb could be shut off.
 * Owlman failed big time. First: Multiverse was destroyed several times before, and he was too preoccupied to notice. In our universe (which is not part of their universe) it's called - Retcon was it?
 * No his entire point was how the only choice one could make would be to destroy Earth Prime, because it would be the only action that would not spawn a mirror unniverse

The QED was an Owlman Gambit that failed.
He's the equivalent of Batman, and so must have the equivalent of Batman Gambits. And why would he want to wipe everyone out?
 * And accomplish what exactly? He made no demands and he knew this move would alienate him from the Syndicate. If he simply wanted to take over a new world, he would have gone to one with something worth conquering. If there was some other motive we would have at least gotten a hint. He really did want to destroy everything and his motivation for doing so was sufficient (assuming he believed his theory, which it seemed like he did, after all he didn't even try to stop the detonation after his bomb was moved to the wrong world.)
 * Thinking about it, the only thing he could hope to accomplish with this move would be to maintain the balance between the Syndicate and the world's governments by detonating the QED harmlessly off world. But again we get nothing to indicate that this is his plan.

Earth Prime really is Earth Prime.
Superboy-Prime lives there, after all, and we all know how irritable he can be. Taking into account his most recent misadventure, it doesn't take a whole lot of imagination to guess what happened. Nekron was defeated and BL-Laurie was destroyed before she could kill him. In a rage, he laid waste to the Earth and set out to do the same to a defenseless universe.

Rose Wilson's mother was anti-Syndicate.
The real reason why she was assassinated. All the more reason why Rose decided its time to stand up against them. The reason why Slade tries to talk her out of it because she doesn't want her to end up dead like her mother. Rose blames her father for her death, in a way, because he had the power to stop them but chose to bow down to their demands.
 * How is this a wild guess? I thought it was pretty clear within the movie itself that Slade's wife was killed by Ultraman because she 'had a mouth on her'.

Johnny Quick's other "counterpart" is Owen Mercer
In comics canon, Owen is the long-lost son of the blindingly Australian George Harkness/Captain Boomerang, and apparently inherited superspeed from his mother's side of the family. Superficially, he's a redhead like Johnny (and Wally). Maybe on this Earth, instead of being adopted by the American Mercers, Owen was raised by his father's family in Australia. Instead of ending his life, he helps save the multiverse through Redemption Equals Death.

This might mean his legal name is John Harkness.

Had the film still been "officially" part of DCAU by the time it was completed, a Justice Lords reference would've been inevitable.
Basically a "we've encountered alternate versions of ourselves before, but they weren't exactly evil but rather too extreme" line somewhere in there.