Instead, it seems to me that some extra choices are often missing or misplaced.
To go or not to go to Bella is not a choice, if then arrived there MC does something that was not budgeted for. the choice should have been "thank you/say goodbye to Bella and leave" and "push for something more," this way I am deciding what happens
Bella is the only LIs we can find ourselves involved with without any direct choice, just visit her in the library and then without doing anything accept her help with the room
Yeah, Bella's path is very weird, to the point that even the official walkthrough doesn't mention that not going to see Bella in Episode 3 will lock you out of her path forever.
I still think it's meant to reflect the way the two of them are drawn together by a raw, inexplicable passion that overwhelms their rational thought, and thus the romance will happen unless you completely isolate yourself from Bella. But IMHO that is *not* communicated by their actions or dialog, it can only be inferred from the size and shape of the void in the story.
Does the ending scene with Sage in the interlude happens to everyone or only for those who have fucked Jade?
Sadly, yes, it's universal. Though an MC who banged Jade will at least look
slightly more concerned about the situation when staring into the mirror prior to that, which is something.