I don't believe he is. He may have been downloaded with Jor-El's memories, but I think he was truthful in "Zod" when he said he no longer felt "his presence". Jor-El's spirit is no longer with him. All of his actions are purely Lionel, only now he is armed with Jor-El's knowledge.

Yes, I saw that on rewatch--though I think we're still supposed to be seeing a sort of Jor-Ellian influence on Lionel, mitigating some of his natural sociopathy. I think it's supposed to be in between the possession and simple knowledge that was downloaded.

And I think I'm starting to lean toward Lex faking the pregnancy, too, after rewatching that scene.