My guesses would be (because Kdrama ha ha):
1) Nam Shin III sacrifices himself or is kill switched and it turns into a Pinocchio type of ending. Where they save his consciousness and after a few years because of advanced technology it allows them to transfer it into a real body. Or some technical miracle happens and he evolves himself to be "alive".
2) So bong ends up dying and her conscious is transferred into an android body.
3) Nam Shin and Nam Shin III are integrated into one body where their memories and consciousness merges. The whole you complete me ideology. (If you have seen Hyde, Jekyll and Me it might be like Robin and Seo Jin personalities merged to make a complete person. It's not the same thing but similar)
4) Nam Shin III sacrifices himself but they bring him back upgraded with a open ending. He is with So Bong when he comes back to life but they don't go into details. Just that he is back and everyone is happy.
5) Nam Shin III consciousness is transfered into the human body of someone else. So he might look different but be the same.
As for the kill switch I kind of think it might be one of those situations where it's used but since he is "alive" not a machine he overcomes it intact to save the day most likely to self sacrifice. I'm sure it will be utilized but I wouldn't be surprised if a miracle doesn't happen and he comes back to life despite. I'm kind of a sucker for the Pinocchio ideas because they make you reconsider what it means to be human and no one has to be sacrificed. But I also like the consciousness merge because they would both be human at the end and share childhood memories on. The son and mother would never have really been apart. Ha ha I tend to over think things though so probably not!