SPOILER warning for today's Action Comics #975.
Okay, so...
Mxy was trapped by Mr. Oz, then escaped and "hid" as Fake Clark.
He realizes who he is, erases the Smith House (perhaps also meaning their time there as "The Whites") and then abducts Jon.
My take on this is that Mxy has been responsible for far more than just being Fake Clark and taking Jon. He's clearly determined to get revenge on Superman.
I'm starting to wonder is Mxy is responsbile for Superman Blue/Red.
Think about it: it's been 21 years and we have yet to see a satisfactory explanation for the Superman Blue/Red stories. The story itself wasn't clear how it all happened.
We know Johns was behind Superman Reborn (and all of Rebirth, even just in plotting/giving story points) and that he loves explaining things from past continuity.
So, Mxy is behind Blue/Red, not for the sake of revenge (though it could be, since he's not beholden to time) and then he needs to create a new "plaything" since Superman is gone. He creates the New 52 Superman and Lois from the same energy he used to create Superman Blue and Red, thus explaining New 52 Superman and Lois's deaths and Lois and Lana's powers.
I also get the impression that Mxy may be behind Rebirth itself, or at least very large portions of it. Is he working with Manhattan? Did he perhaps assist Manhattan in manipulating Flashpoint to create the New 52?
Mxy might be working with Manhattan as a way of getting revenge on Clark. Meanwhile, Oz had his own plans for Superman. Could be Oz was behind bringing Clark, Lois, and Jon to their original (though altered) Earth after their journey to COIE.