That's been my thought. Bendis may not have been able to explain Jor-El's arrival without spoiling elements of other stories that haven't finished yet. Can't really blame Bendis for that.
Or it could just be a case of Bendis being Bendis.
That's about the only real issue I have with the "Jor takes Jon for a summer in space" thing; how Jor got away from "him" in the first place. Everything else? It tracks. Clark and Lois let Jon go on crazy adventures through space and time with Damian, and that kid is a little psychopath. Jor at least knew his way around. And Clark was doing all kinds of crazy stuff without the Kents' knowledge or permission when he was only a little older than Jon; all those weekend trips to the far future where his parents had no way to contact him or get him home, when they knew he had left at all.
Parenting isn't really a Kent strength. They all let their kids get away with stuff most of us wouldn't. They've got a real Darwinian approach to raising children.