What we know from Selebus may already address some of your concerns.
When we get to the purity path part of the game, you'll be given the option to choose one of the girls, and you'll play through that girl's purity path to get their purity ending. At that point, the game will take you back to the decision point, where you can pick another girl. So that's your "start from here" point that you mentioned.
What we don't know is if the bad uncle/bad homie flags are content locks that forever deny you access to an ending, or if they're branches that lead to the same location by different methods. I haven't tried bad homie to see how that plays out in later Rin events, but I could see a narrative path where Sensei has to work much harder to get there than he does under the good homie path. Yeah, you won't be able to see all content in one playthrough, but if there are enough of these either/or story routes, even if they ultimately lead to the same destination, it adds a layer of replayability.
As for the cheater flag, we have no idea what that does. It could be a giant fake-out, it could just result in the game becoming more passive aggressive in the narration, or it could actually impact continuity. We won't know until he actually implements that impact.