Hmm, I don't know either way about the inconsistent point-checks part, but I'll take your word for it.
In my mind there's not much value in treating it as a puzzle/grind game where you need to make perfect choices to reach the specific endings - the payoff is too far away from the place you make the choice, and the routes are very complex (as we discussed). I think the built-in "easy going" mode (whatever it's called) where you get double points is more fun to play because then you can just role-play a character and see where your choices take you, without needing to worry about metagaming the points.