I don’t think it means Doomsday Clock is out of continuity or an alternate reality. If that were true then Wonder Woman #750 which Snyder wrote part of wouldn’t make sense, Bendis wouldn’t be using the Kents, and The JSA wouldn’t be appearing in Shazam. I think it’s more of acknowledgement that something is wrong when it comes to cohesive existence and timeline when taken into account that things don’t fit together. For example in Justice League it’s written that Aquaman’s been believed to bed and just reappeared in the Doom War, but that’s not what is going on in his solo series where he at the same time the sigil went up he’s fighting Black Manta. Or Action Comics where somehow Apex Lex and the Legion of Doom are teaming up with Leviathan to attack Metropolis when that doesn’t add up to when that’d even be happening in this story. It’s acknowledging hey not all the stories are lining up even though they all effect continuity or stories.