I don't think there can be other way though. If they leave the twelve as their own being, then they'll have to answer the question why did the twelve not intervene during the first final day. The Ancient was already pretty much god like, and if the twelve are true divine being even beyond them, that'll be a pretty big plot hole. As far as the storyboard goes, I don't think it's lazy, just make sense if Venat had a plan beside simply nuke the world with the sunder and left to its own device. The philosophy behind the twelve method of of operation also fit well how she wants to prep mankind to ultimately face the End Singer.
The issue is, like I said, the "way" FF14 tell its story. I had said only during the launch story arch that you legit see an appropriate amount of effort put in. But that's pretty much done as soon as the credit roll. The next 3 years, the "after story" portion in the next 3 years are just given very plainly. Even if the storyline is good, even if it's logical, the delivery is very much lazy. There usually no build up, no prep, most of the time we have a new random NPC that we have no connection just stop by, talk a handful of line and we're somehow got drag to the next earth shaking adventure.
And most zarring part about this particular story line is it feels like no one really give a crap about meeting the twelves. Like Ghara came back with the contraption and he seems to put more emphasis on making sure to return it safely because the forum only "loan" it to them. Like ... really? We're meeting "the" twelve Gods here, you would think as soon as the world got out everyone will pool resource into an expedition, not treating it as a favor for a side project. Like seriously, I think the only reason they put that over-excited fem-roe in there (to the point of cringe) is an effort to instill the kind of excitement they think people should have about the storyline but know only a few would.
tl;dr: the after story cycle of FF14 is like a counting only on the lyric to carry the performance while putting in minimum effort in the stage and instrument itself, and it has been this way since 2.0.