Wholeheartedly agree and I like how you put all of this, but I wanna point out one thing I think you touch on and have mastered but never state here: Loss of control.
Spoilers below: HEAVY SPOILERS
The whole interaction with Glitch FUCKED ME UP. Like I lost sleep. This is not a bad thing. Far from it. The Zonebaiting scene is also one of my favorite scenes in the VN for a similar reason. Between the sound design and descriptions there's a VISCERAL quality that strips the reader and Alex of all control and yet... We keep going. We keep sailing the black seas of eternity. We turn that page. It's like reading a Junji Ito comic. We know there's going to be a horrible full page illustration lovingly rendering the horrific but we turn the page anyway.
The unknown isn't just terrifying, it's addicting. We need to learn more and chasing that need will eventually scar us. I honestly kind of hope there's an ending where Alex becomes those scars, where he has the choice to turn back or become a monster and he chooses monstrosity. Or maybe it only looks that way from the outside. A new perspective that makes him inhuman from the perspectives of others. Because what is an adult to a child but a quasi-eldritch and/or fey being that follows rules they can't really fathom.
Anyway waxing lyrical aside great VN and if I were to rerank it post Boneyard it'd be an easy 10/10 for me.