Once you are compatible with eLVL chunks, you could dump the alpha-channel, or additional custom tileset with alpha channel in a eLVL chunk.To minimize filesize, you could have the RGB data in a standard bitmap, and only the alpha-channel as a 8bit bitmap in the eLVL data. This gives you full backward-compatibility for other clients to work with maps that support it, and full foward-compatibility for your client to open older maps. The easy way would be to leave the bitmap tileset, and put a full PNG with alpha channel in a eLVL chunk. But you get a lot of duplicated data that way.