Quick update:
mds5_i and ealin_12 were patched, following luksy's remarks, with corrections on the fonts used for the writings (Japanese instead of Chinese), as well as corrections on the book titles on ealin_12. New versions have been uploaded on the repo.
Otherwise, I've been working on the layering of mds5_w, which was another pain in the butt. I have all the alpha-masks ready for the layers. All I need is to finish a couple of textures (notes and posters stuck to the shelf and behind the seat on the left), make the final render and then it should be straightforward. Hopefully the remaining scenes (5min_1, 5min_2, and mds5_m) should be much less complicated to layer and cut out - I'm just missing a couple of textures in each of these scenes.
Since my adventures with the rendering and layering of mds5_1, my workflow has changed a little: I make a rough alpha-test render (with small amount of samples), which I use to prepare the layers. Depending on the results, the modelling may have to change (objects added, or moved), especially if we're in the case of "space not displayed by background layer, not covered by foreground objects". I go through the iterative process Model > Rough render > Cut and layer > test in game until the layering in the game fits the desired result. All that needs to be done afterwards is to make one final render (with lots of samples for high quality), then use the layer cuts from the rough renders as alpha masks on the final render to generate the layers in high quality quickly. Add post-processing effects (light glows, god rays, etc.) and there you have it.