I'm going to open this with I have never seen an RPG Maker game like yours before. Structurally, you can tell, but the way your story and mechanics go, I think it really stands out. I did not really see the theme until quite a way in, but I loved the twist.
I found the game to be on the difficult side once I hit Layer 4, but that could be just how slow my reaction time is to an active battle system. My biggest critique is the red menus and message boxes got hard on my eyes. I can only suggest that in the future you ask a couple of people who haven't been staring at it the whole time to see if it looks readable. Red is a very powerful color, and getting a balance between a good shade that fits your theme and is also readable can be difficult, especially since the color wheel in the RPG Maker database looks nothing like the actual menus in the game. I'm sorry if that sounded picky, but the database is such a liar with color.
Overall, I thought the hook was a little weak in the beginning of the story, but that dungeon was amazing and sucked me right in. Like walk into that first bit of sludge, and wow. It really made me eager to explore your creative dungeon. I'm glad I got as far as I did, because being left with that twist was amazing. This is a very solid game, I mean, the worst comment I have is about something like window color, and that the intro was slow. This one was fun and that's the best part. Thank you for creating this.