I was wondering if it would be possible to actually render multiple Z-layers through the BYOND engine by default without the need for tricky and often sub-par custom systems.

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_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!

Seconded. With this isometric-ness popping up, I would like to be able to render my skyscrapers properly, with icon-less tiles (and semi-transparent tiles) allowing you to see to the previous z-level (to a certain max).
I take it that you're going for a similar idea as Data described in [link]?
(Similar as in the possible benefit, not the actual implementation)

If so, I'd love to see this happen.