You should save the game archive after at least three or four updates.
If you've played the game carefully, you'll notice that the author does NOT remake it, he shows DIFFERENT OPTIONS of events, with different alternative solutions.
For example: in update 0.32 we see ALL the scenes from the Cuckold's side. Whereas the previous version was closer to Netori, if I'm not mistaken.
So, if we combine version 0.31 and 0.32, we get a game with the possibility to choose who to be.
If we add one of the earlier versions, where the story goes from the beginning, we get a full version of the game with a choice.
In other words, the author is trying to mess with our heads.
However, it is quite easy to follow his logic.