The main issue I have is with auto-tiles. Check this screenshot out:

Notice the tiles for the wall are not auto-tiling; you can see what they should look like in the window on the right.
I looked at the script from this thread, but it seems depressingly complicated to manually calculate which of the 24-48 auto-tile values I have to set. Is that really the only way to do this?
I'm setting tile data directly by using $game_map.data[x, y, 0] = tile_id. (I require a pre-populated map with a single, stand-alone tile in the first tile location so I can get the ID.)