I did try; after about two minutes getting ancnt1 to appear, which looks great now without the black areas, I tried another, and about ten minutes later and 375MB+ memory usage I had to restart.
Anyways, not having a save game to hand I've just photoshopped a few of the backgrounds to illustrate what's left. Note that these were what I noticed on the previous version so I don't know if the new version has these or not:
The semi-transparent blue 'crystal' foreground piece is missing from the central area.
Try this out ingame and see the glowing effects all over Wall Market; I just felt the area on the left was most prominent. They're transparent foreground bits, simulating lighting. I know these are made using palette opcodes in the script, and as a result I think they need to be set up in the foreground sprites so that you can manipulate the colours correctly via scripting. Any insight would be really useful.
[Edit] I did actually make a mod to the background generation code that outlined any 16x16 tiles using the "unknown_sfx" as per fice's documentation, and I'm fairly sure these are the ones that set the "light" areas (since, for example, on Aeris' house, the rays of light coming in from the top left where outlined in the same shape they are in the game for the lighting areas). Still not having peeked into the palette manipulation opcodes as yet, I'm not sure whether the numbers for unknown_sfx correlate with those used by the opcodes.