At first I kind of shrugged this off thinking "well, there'd just be no way even Bendis would do that." But then I remembered Siegel and Shuster literally started Superman out as not being an alien, but rather being from so far in the future that he may as well be an alien. Mark Millar (at the recommendation of Grant Morrison) put this in as Red Son's twist time loop ending.
If subconsciously Clark has been dealing with all the complications of being a Kryptonian (Kara also going through major complication too), and during the rebuilding of the DCU he has to relive both the death of Krypton and Oz being a thing, who's to say he doesn't have a moment of weakness and say "maybe if I were human this would all be simpler?" It's a halfhearted thought, but the DCU is in such a sate and Superman is in such a position of power that it goes through.
And thinking on it more, this would fit with Bendis' more socially conscious writing style. The idea of an immigrant, person of a specific race, sexual orientation, or religion having a moment where they thing "wouldn't it just be simpler to not be what I am right now?" That's powerful and relatable stuff.
Not sure if Jon is powerless though given he's still good enough friends with Damian to rock out with him at the end of Metal post-rebuilt DCU.
In any case, this would check all the "bigger change than crisis" boxes in a more direct way, it would be steeped in reverence for Siegel and Shuster, and would allow for a character arc and unfolding mystery.