His July Word Balloon interview touches on Doomsday Clock. At around the 2:29:00 mark Bendis says he doesn't talk about Doomsday Clock much because he's "desperate" not to spoil anything on Geoff Johns thing, but (and this is the big part) "there's stuff going on in my books, that when Doomsday Clock is revealed you'll go OH!" "So, yes for people who want to know. Yes, that will connect. But how and why and in what shape and what characters, I won't comment." Then he's asked about Jor El and immediately changes the subject.
Now, I have no doubt Lois will end up back at the Planet, but she was at the Planet in Heroes in Crisis 2, and Doomsday Clock. That's minor stuff. But Jor El's status remains the biggest issue, since the way everyone reacts to him in Man of Steel is simply not consistent with his last appearance in Action, since he presumably should be imprisoned by Manhattan at that point.
Man of Steel occuring after the conclusion of Doomsday Clock makes the shorts the only continuity issue and clears up Lois's appearances in both as well as Jor El's appearances in Man of Steel.
He replied to a tweet about how someone didn't see how people could read them as heading for a divorce by saying there were some "genuine bullshit headlines" about the issue, so I do think he is annoyed by some of the reaction since he saw this as a positive and romantic statement on their love and not setting up any type of drama.
But it's his execution that leaves open that interpretation. One partner telling the other they need space to rediscover themselves is a cliche, and in fiction, typically ends up in one or both partners realizing they are better off alone. He really should not be to taken aback that its being interpreted that way by people. I personally don't think that was his intent, but the execution was muddled enough that that interpretation is not outside the realm of plausible.