I'm assuming each area is its own large layout, and you're using something similar to, if not exactly, the map masking and transition affects in the MagiCam Plugin, with various amount of tweaking.
The control config was a nice touch, as remapping with the Input System Plugin is a godsend. At first I was surprised you said you didn't use any Python scripting, but then looking at how the config behaved I'm not surprised. In my current project I allow the user to remap at any time while playing. Due to the Binary Object being rather bugged, I instead do all my binary writing via Python. This allows me full control of the file writing, plus I do a lot of formatting on the data for various display purposes.
I love looking at these games and trying to figure out what systems are in place. Plus, being a Metroid fan and a lover of all things pixel, this game is one of the most glorious things I've ever seen. Amazing work.