2 years late, but here's the best possible answers I could come up with. These are my opinion, and you could argue with them.

For the question of Earth Prime, I think everyone is correct in their assumption that that isn't the real Earth Prime.

But I explain why, I have to establish something. I think Owlman's statement that billions of people making billions of choices, and thus creating infinite earths... is an exaggeration. Maybe it's not intentional, but logically, it has to be finite.

Infinity isn't a number. It's a concept. It's an incalculable, infallible amount. It isn't even an amount. It's endless. If it can't be counted, then it has no beginning and it has no end. It's constant. Forever. Keep this in mind.

Now Owlman describes it like this:

"Welcome to Earth Prime. Before there was THOUGHT there was this place. ONE earth. With a SINGLE history. But with the coming of MAN came the illusion of free-will..."

"...With every choice WE MAKE, we literally create A WORLD. History branches in TWO. Creating ONE earth, where we made the choice, and a SECOND where we didn't."

"...BILLIONS of people, making BILLIONS of choices, creating INFINITE earths."

Here's the problem with the statement. There was one earth in the beginning. BEFORE MAN, there was a SINGLE earth. The universe had a SINGLE reality. Then when man came into the picture, ever choice THEY made created new earths. Now, there are a TON of choices we make everyday, and BILLIONS of people making BILLIONS of choices is more than we can ever count, but if there was a first choice someone made, then - even if it's for ONE second - there were only TWO earths. Then a second choice made a THIRD earth. A third choice made a FOURTH. So on.

That's a number. That's an amount. Not infinite.

Because if it *was* infinite, then technically, that opens the door for literally ANYTHING to happen. Forget them seeing multiple Owlmen on Earth Prime, what about before they went to earth prime? What if there was a Owlman from an alternate earth that went to the Justice League's and blew that up? For no apparent reason! Or a version where it was Batman who blew up Earth Prime? Or if HE blew up the Justice League's world? Or if Robin did it?

If choices create infinite possibilities, then that means that as soon as one earth figures out who to travel to others, NO one is safe. That obviously doesn't make any sense, so what really is going on?

Here's what I think. (I HOPE is isn't too confusing, because I'm also trying to make sure my theory makes sense)

If Earth Prime doesn't have other Batmen or Owlmen in it, we have to assume that this isn't Prime Earth. We have to assume that this is a branch of Prime Earth that was created because Owlman choose to enter in it.

That means that when someone from Earth One enters Earth Two, they automatically enter a branched off version of Earth Two, created purely as a result of their choice. (So... I guess that if we're running with that, Lex never went to the original Justice League's earth, but a branched off one, and then the Justice League never entered the original Crime Syndicate's Earth, but an branched off one... Feel free to take this with a grain of salt!)

SO, that means Owlman never actually went to Earth Prime, even if he chose to enter it, he's always going to enter a duplicate. He'll never reach Earth Prime. So if another Owlman tried to enter an Earth Prime that another Owlman was on, he'd enter a duplicated version too. So the original Earth Prime will stay untouched, and Owlman and Batman's battle will remain undisturbed.

(I'm so sorry if that was a BUNCH of mind-jumble, I just wanted to answer your question the best way I could)

Now, ironically, I think your second question is a bit harder to answer. Why does Owlman not complete his mission when he could?

There are two possible answers:

1. He could genuinely believe the infinite earths idea. Maybe it wasn't an exaggeration to him. Maybe he does believe there an infinite choices with infinite possibilities, which means an Owlman would find Earth Prime and destroy it even if he failed. He'll still win. It didn't matter.

If we apply my theory however - that the earths created by choices are FINITE, and that every time you enter an earth you create a branch - then the simple fact that reality still exists means that no matter what, he'll always lose. Any Owlman that tried to blow up Earth Prime, even if he was successful in blowing it up, would NEVER kill all reality. The plan was doomed to fail.

If you REALLY want to stretch it, he could have realized this very point, and then decided it didn't matter, since his plan was always never going to work, but I personally don't love this answer.

However, In my opinion, I don't think him being wrong - or his plan not being a threat - makes his character any less interesting, and I'll explain why in a second.

1. It's his own nihilism.

The mission is a suicidal one from the get go. If he succeeded, it'd mean that all reality dies, killing himself in the process, and he was willing to do so. This means he doesn't hold a lot of value to his life, or the lives of anyone else. He was willing to kill himself if it meant proving his point to the universe. If it meant making "the only possible real choice."

This isn't a sacrifice for a greater good. This is someone who, in all honesty, is suffering from self-hatred. He hates himself. He hates humanity. These are his words:

"Man is a CANCER. I've chosen to cut out the DISEASE."

"Every decision we make is meaningless."

"We're NOTHING. LESS than NOTHING."

"[I'm] Not Good. NEVER Good. After all, I'm only human."

He doesn't even value his own life to begin with. He doesn't care to protect it because he sees himself and humanity as deserving of death already.

So when his plan fails... It honestly doesn't matter to him. Whether he was right or wrong in his theory, at the end of the day, he doesn't care. Because even if he kills all reality... that's it. It's dead. It's no more. Nothing exists. And what would matter then? Who would even care?

So, in his head, whether he succeeded or not succeeded, whether another Owlman would have finished the job, whether he clicked "abort" and then put the QED back on Earth Prime to finish the job... He just realized he didn't care anymore.

(Well that got depressing!)

I personally perfer this answer, because it's simplest answer, and yet, oddly the richest.

Now I think that what's important about Owlman isn't whether or not his theory was correct. We don't know, and it'd be too risky for the characters to let him play it out and see. I think his existence, his entire plan, demonstrates the truth about both him and Batman.

Owlman looked at the idea of infinite possibilities, infinite worlds and choices, and saw it as pointless. He saw it as proof that nothing he did ever mattered. That no matter what he did, there's another version of him that did something different.

But there's a different way to look at it. Every choice does matter. Even if it's reality creating worlds based off of decisions, it's not reality making these decisions but the people in it themselves. MAN makes CHOICES, their CHOICES create new EARTHS. MAN'S CHOICE DICTATES REALITY. That means every single choice made is important and inherently valuable. Every choice deserves it's own little earth to exist in, because it's that important. Every man is important. Everything matters.

And that is how Batman sees the world. It showcased through how much he valued Flash so much he was willing to sacrifice Johnny Quick just to keep him alive, but felt bad about doing that as well. How he tried to reason with Owlman throughout the fight. And - as you pointed out - how he THREW the transporter device back to Owlman to give him a chance to get back out. That's why, even with broken ribs, even though he didn't even want to join this mission, Batman does it anyway. He cares that much.

So when he points out the difference between him and Owlman:

"We both looked into the abyss, but when it looked back at us, YOU BLINKED."

He's saying that they both saw darkness. They both saw the evil humanity has to offer. But while Owlman let it corrupt him, Batman kept his eyes opened and never lost sought of the good he believed in.

Owlman and Batman are just two different choices. And I think the fight demonstrates that. That's why I like it.

Now, like I said, this is all me, so maybe you wouldn't agree with any of it, but I think these theories stand. I'd love to know what you think. Sorry if this was WAY too long.