Ya this was discussed on the talk page for those issues. Their appearances r set in the past, which is how Jon grew up there before coming back. As for the paet where Superman said they r the rulers of earth 3, its a typo. They were the rulers until earth 3 was destroyed and they all died.
No, it's very strange that they did not come back, since when Jon appeared in the Prime Earth, they were already dead, and when he traveled with his grandfather and was sucked by the wormhole, they came back.