I thought it was implied that the general was a natural, accidental baby. If Lyta married and got permission to procreate with someone, it would have been a known thing in some public records database, or at least gossiped about. The fact that General Zod had no way of knowing because Lyta never told him, and that she was apparently single (and grouchy) the whole time, seemed to suggest it happened the last time she and Seg were together.
If that's a thing, and the baby can still be a full member of your house, then why Nyssa was worried about baby "permission" in 1.01 is a little bit of a mystery. But the show likes to contradict itself like that. Some epic moments in this finale, though. I loved Adam wandering around Brainiac-frozen Detroit.