Didn't see this thread until now.
Pretty fine with whatever story is agreed upon, right now more focused which formula this game is gonna go by (Amount of cutscenes, Sequances, the S-link conversations and so on).
As for the Violet room and the entity, wouldn't it be best to just have a voice fill the room? While it might sound like a lazy way of not drawing a character, it personally seems more intriguing if the voice is all the player has to go off. Then maybe later the voice makes a reveal if the story so demands.