Hello! I took some time to reverse-engineer all of the .dat files in the /data/ folder (with the exception of scripts.dat, which contains the map warp data)
https://www.mediafire.com/file/c81v2pfmtp1pcw7/La-Mulana_Classic_Maps.zip
I'm hoping it will somehow help with the routing: it turns out that all the maps are actually groups of 4x5 rooms, and using Cheat Engine to go through the walls seems to wrap the map around exactly how the .dats tile the maps in memory, unless there's a door or ladder that leads somewhere else.
In the .zip, I've included both .png and .tmx (Tiled) formats, along with the tilesets for viewing the maps in Tiled.
EDIT: For those who want to reproduce this, here's the C# source code:
https://www.mediafire.com/file/ylqj22j9dpca6y0/LaMulanaMapViewer_src.zip
It's written in C# using Visual Studio 2018. After running it, you can open a .dat and it'll construct an entire .tmx in the debug console: Just save it as a text document and change the extension to .tmx, then open it in Tiled. The tilesets are loaded at "./tilesets/" relative to where the .tmx is, and they come from the original game's /graphics/ folder.
EDIT2: Fun little trivia, it seems an official wallpaper of the remake suggests the remake's maps are stored into memory similarly:
https://la-mulana.com/img/desktop/lm4-1280-800.jpg