Because when you think about, given how the story goes, it's not a pick-and-choose game. You can't just say "oh, I'll take X in my harem, but I'll let Y get NTR'd" because all stories get interwoven at some point. You make your choice at the start, so the two storylines run next to each other. Sure, they'll follow the same story beats, but they'll never intersect. So, if you look at it from a technical point of view, that's two different stories in the same setting, which means double checks for each event, making bug tracking harder. It's a lot easier to restart from scratch and re-using assets.