I don't know how to solve the alpha problem in the tile but if i deal with that problem what i would do is create in the tileset have different version of the same tile and change in code between them.
like this (3 different version of the same tile)
and if i need multiple alphas and don't want to do multiple sets for every one maybe i create like 3 tilemaps, change alpha tile maps, and load the tileset in the map wiht more alpha if you are closer. And load in the tilemap with less alpha if you are far.
I don't know if this have sense in your game. ._. In the image i have 3 tilemaps with different alpha, i use the tilemap with more alpha for the tiles are closer, tilemap "2" in the middle distance and "3" far distance