Alright, I'll try to not sound like a soyface youtube lore implication deep dive analyst, BUT...
I went in pretty much blind. Maybe with a bit of prejudice because of renpy. And the first playthrough was enjoyable. Laughed a bit, cringed a bit, there was this decent sort of mystery, some creepy intermissions here and there. And then it closed (or crashed)? And since one of the lines told me I could go and poke around your game files - well, how kind of you, I was planning on doing that anyway.
And then I see a shit ton of content that I haven't encountered. I could also see your carefully placed memes. Dunno why. Considering where your game went afterwards - I would think it wasn't you just treating a curious gamer with some funny images, but trying to gaslight him into thinking "those are probably unused assets, huh".
But then I restarted the game, and stuff changed. And it became way, way creepier. I was skipping read dialogue, so all the extra changes you've placed were hitting me one after another. And I gotta say - it was very, very intriguing. It's hard to explain, but... Kinda like "I think all the pieces fit and I have an answer, but also I think that it's not correct because the pieces didn't fit perfectly". Which is absolutely awesome.
And... I think the dialogue made sense. Kinda? I think I have a hint of what the answer is, and I think it should explain why Jojo is so... Well, you know. Again, I don't want to write my answer because very clearly the story is not complete (yeah, I saw you planning an Act3 in rpy files), but I'm so invested. Even though some shit legit disturbed me, and I absolutely can't stand horror.
I think I saw most of what you have. I know I missed at least 2 scenes, but I have no idea how to reach them. But man, you have me hooked.
Great stuff, absolutely fantastic.