-As it turns out, Jon was the only one to get sucked through the wormhole.

-Jor was beside himself because he thought Jon had actually run away from him. According to Jor, he made deals, stooped to certain "lengths and depths" in search of him. I'm assuming this took years until he figured out what really happened and even then it still took a while to actually trace where and when Jon had disappeared to. He tells Jon that he never gave up searching for him, shredding even more of Jor-El's frayed mind no doubt.

-Jon doesn't appear to fully grasp the severity of his situation, not even after being locked away in a volcano for years and then trying to get away from the super powered evil version of his mother.

-Jor gifts Jon with a super suit and immediately after, their ship gets attacked by Zaar, Zod and Jax-Ur at which point Jor transports Jon straight back to earth where he went looking for his parents and we catch up with the present.

-Clark and Jon decide to go in search of Jor-El and Jon's suit suddenly lights up and throws them in the middle of an intergalactic battle, Jor's ship smack in the middle of it. I think Jor fitted the suit with some sort of GPS/beacon to help him find his way, or I could be reading too much into the art.

I think the "deals" and "lengths and depths" Jor made in the undetermined past while searching for Jon are what inadvertently created Rogal Zaar and now explains why Zod has now switched sides suddenly.