These things like certain characters acting differently or saying things like what Makoto said are not happening in the reality of the game, only in his head. It happens quite often in other fiction where the MC imagines an entirely different outcome or spoken line than what is actually said or what actually happens. This is why Makoto's jump in "Bluejay" gets reversed, because it never actually happened, though her disappearance and short lived change in behavior did. As player Sensei slowly starts to break down further, something Noriko is exacerbating and Maya is trying to prevent, he sees more and more terrible things begin to happen, but in reality, everyone is just fine. It is only him that is truly suffering. That said, the conditions each girl suffers from, like Rin's depression, are not part of this breakdown, they are quite real. Back on the USER theory, USER2 seems to be a more gentle and caring personality than the other USER, not sure which USER the other is. When we see him actually try to help, that's USER2, but the one trying to get into the girls' panties is the other USER, a USER willing to do anything short of an actual crime at the moment because he knows anything the girls perceive as bad would actual be a detrimental action. Furthermore, because of the more gentle actions of USER2, that gives me reason to believe USER2 is old Sensei, the one from before the events of the game. That's my current theory on the USER situation and what is happening as far as weird moments in the story, anyway.