The first time I tried this one at the beginning of the project, it was a catastrophe. I wasn't aware that the background colour bled into the map tiles and therefore corrupted everything.
Of course I couldn't submit a trainwreck like this, so I put it on hold until I was able to find a better approach.
vSNES can differentiate between bg colour and map tile colours and separate them, but it's tedious since you need a new quicksave everytime.
Then I found out that you can activate the tilemap viewer in bsnes-rawpalettes by selecting
Tools - Debugger - S-PPU - Tilemap Viewer
Then you get this:
Most important options are
"Auto update" and
"Override Background Colour", also changing the bg layers (up to 4 layers viewable, Rudra usually has 3).
Effect toggle doesn't do anything for the tilemap viewer, it separates automatically so you can leave all the check marks in place.
There is one downside, though: It has a fancy way to display the map, which means its kinda chopped up. You kinda have to know where one area starts and where one ends, this changes as you move on the map.
I solved it for me by screenshotting the whole map + layers first, then replacing the tile-eating bg colour with screencaps from the tilemap viewer.