Knight said:I took it as Batman talking about the "now" and not when it happened.
Batman's exact words were "Two of them were already on the Watchtower."
So he was talking about when it was fired. Which means, to me, he is referring to J'onn and the Atom.
I found it weird that he didn't include himself in that scenerio also. Batman would know that Watchtower inside and out I would think, and be able to do it too. Why he wasn't part of that....who knows? He is certainly smart enough to do it if he wanted to.