I won't talk about what JJ2 supports, because people (Violet) keep finding out that it does some pretty weird and unexpected things. JCS tileset compiler anyway, supports only 0% and 100% transparency. The only way to make something partially transparent is the "Translucent" type of tile (the transparency is about 40% then, to make it lower you can use other layers and you can't make it higher). Also, take a note that the Translucent tiles still use only the existing palette entries.

This is one of the things which keeps the tiles graphics impossible to make perfect and as a tileset maker you will have to deal with this. The others are: palette, tiles limit and layers limit.