A part of me really wonders if the essence of both Zod and Jor-El wasn't somehow downloaded into the single AI program that was sent along with wee!Kal-El's pod and then something happened to dislodge Jor-El's essence from Kal-El's sphere until the events of Covenant.
Yes, I think it's definitely possible that Zod and Jor-El are both present in the pod. But now I am wondering if the crystals were, in fact, a back-up plan for Jor-El. If he really was the one who imprisoned Zod, and he was thinking all along as Earth as a backup for refugee Kryptonians (or at least Kal-El, depending on when this was set in motion), maybe he somehow had a backup of himself in the crystals, and it's been Jor-El rather than Zod controlling Lionel this whole time.
Re: part II
Yes, I think it's definitely possible that Zod and Jor-El are both present in the pod. But now I am wondering if the crystals were, in fact, a back-up plan for Jor-El. If he really was the one who imprisoned Zod, and he was thinking all along as Earth as a backup for refugee Kryptonians (or at least Kal-El, depending on when this was set in motion), maybe he somehow had a backup of himself in the crystals, and it's been Jor-El rather than Zod controlling Lionel this whole time.
I have to think about this some more.