I am not sure where things are confusing on the Zod timeline.
Seg is Jor-El’s father, and it is implied Zod’s father although Zod never knew him because he died before he was born. He was in the phantom zone until around the time Superman was born, hence how Seg is his father and Superman’s grandfather, Zod didn’t age in the Phantom Zone. He presumably was from the present, he knew Krypon blew up in 200 years. If you mean that doesn’t make sense in terms of Seg’s age, Kryptonians like a lot longer then humans. Hence how it is so far away but only 2 generations removed from Superman. I may be missing something, but it all lined up to me.
As for leaving him out of it. Orignally the first pilot didn’t have Adam Strange and the whole time travel aspect. And SyFy hated it and it tested badly with focus groups, so they redid it and added the time travel part figuring it would hold more interest, especially to non-hardcore comic fans if the show had more direct ties to superman then just a political intrigue on an alien planet that sort of tied to Superman a long long time later. Honestly, they were probably right. So even if Zod wasn’t in it they would have had to have someone travel back from the future to try and mess up the timeline so Superman was never born. They could have made it Braniac though I guess.