We do know that Morrison loves to pull from all aspects of the character's past so yeah I wouldn't be surprised if he used the Animated Brainiac...who happens to be one of my favourite incarnations of the character.
I dunno. I like Colu. My favorite Brainiac's still animated, though, but it's not really DCAU, it's its own little bubble--the LSH Brainiac. That is a perfect example of reimagination done right.
Then again, they were making him the nemesis of Brainiac 5, not Superman, so the narrative purposes differ.
Of course, if they used the DCAU Brainiac, Querl really makes even less sense than he already does. "Hi, I'm Hitler 5--no relation."
Here's a fun query: does the colloquialism "brainiac" exist in the DC Universe? Explain your answer.