I don't disagree with you, but I think this won't
necessarily apply, depending on how the dev handles things. The game isn't just going to continue from where it left off. It's basically getting remade, which means thoughts of the MC
might become a regular thing throughout. They also still might not happen at all. I don't know what the plan is ofc, but since I don't believe
Meepish has yet weighed in on specifics like this, it's always possible MC's thoughts will be regularly expressed.
There is at least one way I can think of to do this without changing the flow of the MC relating events to Dr. Amana. It does assume LIs would go into considerable detail later with the MC (though that doesn't need to be in the game, ofc). But he could tell the story as it was conveyed to him, obviously where he himself takes some liberties with extrapolation, assumption, etc., for anything he wasn't specifically told.
Maybe Cassie talks about a discussion in a locker room with some girls at school. She probably won't give him verbatim lines from their conversation, but based on things she said, he might narrate with
some degree of accuracy: "She was a real bitch!"; "Do you know what she said to me?" (followed by a quote); "She said she loved the feeling of fingers against her clit"; etc.
It would be fairly difficult, but it absolutely can be done. I'm not promoting any particular approach to the storytelling or anything. I'm just thinking about some ways of going about different things and remember certain novels I've read, shows I've watched, etc., that might be applicable for specific approaches Meepish might take.