It’s plausible that I’m doing something wrong, but it seems to me that tilemap layers don’t respect the transparent index setting. The first (transparent) tile always uses the colour at index 0 even if the sprite settings denote a different colour as transparent.
So if you’re working in Auto mode you can’t fully paint a tile with the colour at index 0, because as soon as you do, the tile gets merged into the transparent tile and effectively erased.
Actually, I just had another look at your screenshots and maybe my explanation wasn’t entirely clear. In the case where the transparent index is 4, can you paint a tile fully black without it becoming transparent afterwards? Though I suspect yes, because I’m noticing a difference between your screenshot and what I was seeing yesterday: when I had the transparent index at a nonzero value, the 0-index tile still used the 0-index colour.