Doomsday Clock 2 takes place in Post Flashpoint
Doomsday Clock 3 takes place in Post-Crisis and Post Flashpoint
The evidence?
Doomsday Clock 3 goes between an era in which Luthor is clearly not a hero, then evolves into post Flashpoint in which Johnny Thunders is talking about his family and the thinking of the JSA and then goes back to the 80's/90's in which the Joker is out and terrorizing gotham. The major clue is neither Batman nor Luthor have any ideas about Alternate Earths clearly by their skepticism in which is evident by Batman locking up Nu-Rorschach and mocking Luthor mocking Veidt and being Anti-meta. Why would a Luthor who was in the JL and wearing the S stand for that? Am I missing something? Anything else is just red herring IMO. This wouldn't happen to a Batman that has seen what he has seen in a Post-Flashpoint Landscape. Batman is also wearing the old suit and not the yellow outline and purple cape. Manhattan may have landed in The Killing Joke time period and then shaped it to his will. We may see that happen within these pages.
Hence why there is no crowds marching in the street in Doomsday Clock 3 but there is in #2.
I am certain of this. My Dr. Manhattan is the Cosmic Hand plays directly into this. Please see my other threads for details.