thanks for the compliments everyone!
@Air
This probably needs a little explanation that I didn't provide before. You can load the map I made and see very quickly what the black tiles let you do; it's actually a little hard to explain in words, but I'll try. They aren't there at all to be normal, fully visible tiles. Their sole purpose is to go behind the stone tiles, on a dedicated layer, when the stone tiles are being used in their primary (but not only) role, which is to make things like stone bridges/platforms and other structures. It makes the stone tiles look interconnected even though the stone tiles themselves mostly don't go all the way to their tile borders. Two of the black tiles are only little rectangles that take up half a tile. Those are for making end pieces of platforms and other structures, so it looks like the stone tile is connected on one side but not the other. One of the black tiles is to go behind a stone tile that connects to other stone tiles on all 4 sides, one of them on 3 sides, one of them on 2 sides with one horizontal and one vertical connection, one for horizontal-horizontal connections, and one for vertical-vertical. The 3-side and 2-side ones will need to be flipped around by the mapper as needed. The overall effect is actually very nice I think. Now, the reason I decided to do it this way, with the requirement of making 2 layers, is that there are 7 different stone tiles, and when you're making a structure out of them, each of them can be used in a total of 13 different combinations in terms of where the neighboring stone tiles are. So, this is a way of accomplishing that with 14 different tiles rather than 98, saving space in the file and making things a lot easier for the mapper (albeit with the cost of probably being more CPU-intensive). It also has the side benefits that the stone tiles can then be alternately used on a layer above your main "grass and dirt" layer as nice decorations for large sections of dirt, like how the bones are used in grass_main, or you can also build structures or obstacles out of them and just not use the black background tiles, giving a different look (which wasn't the primary intent, so no guarantees on how good it looks, but I think there's some use for it). A side benefit is that like this, someone else can easily come along and change up the color of the black tiles to make stone structures with a different look, ie one that doesn't have the darkish tones that this tileset has in mind, and they don't need the source files to do this without having to push pixels - just make some rectangles of the color you want and you're done.
Also, I don't know what you mean about 3-corned tiles. I don't think I've seen any glitches with these tiles, but maybe I'm missing something?
Thanks for your comments all!