Wasn't actually
too hard, when you put a colour that's nowhere else used in the tileset (like magenta) on a layer below, use colour-select with zero tolerance on the "empty" places with [include all layers] option enabled (or whatever it may be called for other programs) and then remove the selected parts. And then use that one-colour-layer as a mask to remove the excess black from the tileset layer. wooooo.
I hope this now turned out right. Neat tileset btw.
Don't know what program you use for tileset making, but if you use an eraser tool to remove unnecessary background, make sure to have it erase 100%, or some setting alike. Or colour everything you want to have transparent later on in an unused colour like magenta, so that you can use the magic wand and remove stuff that way.