Look... As I said before, it's too early to tell and it's not the best situation ever. I guess that something in this run may be editorially mandated, there are no A-list artists involved and it is even possible, or likely, that everything will be forgotten after the end of the run.
But I seriously think that PKJ may have hit the target in terms of setup. In a way, even if he actually made Jon more powerful than his father it wouldn't be a huge problem, because PKJ's Clark is undeniably the more authoritative and respected of the two Supermen. In a way, Jon is to PKJ's Superman what Superman has been to Batman in a lot of recent comic books and movies. I mean, in the Snyder Cut Batman is less physically powerful than Superman, but he's actually the dominant character, right? Well, it's the same situation here.
I guess that the right move was getting rid of all the Brady Bunch rubbish, the fake lovable atmosphere, and replace it with something a bit more serious and solemn. He didn't turn Superman into Batman - quite the contrary, he created an interesting variation of the Superman family without necessarily copying the exact same situation of the Batman family. There isn't a specific equivalent of Nightwing or Robin, but rather, well, a clan.