Others might have definitive answers, but the best I can provide is that if you're careful with the choices you make you can avoid any negative points with the main LIs while progressing their routes.
There are a ton of variables that are being tracked in this game, and half of them either block off extra scenes or result in an awkward encounter. I've only just worked my way back up to Ch5, but here's the set of choices I've made so far to get better outcomes with the main LIs:
As I play through Ch 5 I'll add more to the list, but for the time being this was the best path I could figure out by looking through the game code.