I mean, it's still clumsily inserted, but I don't think there's a way NOT to have something like what happens there to feel "clumsy". I guess they could refrain from presenting it as a "dream within a dream", but I think that's sort of the point of the overall experience for Bruce. He's not sure whether it's real at first, and that's how Affleck plays it. Then he discovers the metas are out there.
To me, it's the sorta thing we see all the time on TV. Shows like Legion, like Hannibal, like Taboo have a lot of bizarre and mind-f****** imagery that doesn't make sense at first. But we sorta accept that in an episodic format, because we know it'll be paid off later. We know when the next ep is coming. We immediately get a preview for it. And we know exactly how long it'll be in terms of the episode length and the length of the season itself.
That type of thing is a lot newer and harder to pull off with films, as people still expect them to be standalone in a way. They're to have a beginning, a middle, and an end. So BvS is really this 3 hour episode. And you have to wait a few months for the next one, but it ends up being kind of a shorter filler about some other group. So then you gotta wait almost another year for the next ep, except that one is a flashback. Then finally, three eps later, you maybe get a bit of payoff. But truthfully, it won't all make sense until the finale. I don't think JL is the finale for this season of the DCEU. With this slate, it's hard to tell what is though. And as a viewer, that's an understandably frustrating thing to behold.
If I had to guess, I think WB will stay the course. None of this Flashpoint business. Not now at least. I think things will obviously brighten up, but I don't see them basically retconning a few films in. If anything, we'll see more of the Knightmare world and maybe how it started. I'm gonna guess that things were probably much happier and more hopeful at the onset before it all took a hard left. That world will just be the inverse of the DCEU as we currently know it, with things starting dark and gradually getting better. We'll probably see it in a Flash solo.
To me, that's how you payoff everything and give the fans what they want, without having to apologize for all of the work you've already put in.