Perhaps if we had the ability to specify the "z" displacement (z in iso view, y in top-down view) of layers, and a tile type that would be rendered as invisible, or possibly any tile with any alpha transparency as such:
z_format = RENDER_ONE | RENDER_TURF | RENDER_ALPHA
z_offset = 32
Also, for isometry, I think it would be valuable to rotate on the client side, directional icons' facing directions based on the user's client-dir.
Scratch that! You already implemented feature #2!