Idea based on this forum post: http://forum.tilemapkit.com/t/understanding-the-basics-how-to-work-with-sprites-and-faux-3d/52
There should be a mode where the draw order of tiles and any node on tile/object layers depends on their y coordinate. This ensures that for maps with "pseudo depth" (example: http://www.twinfinite.net/wp-content/uploads/2015/03/ultima-online-shack.jpg) the tiles and figures correctly clip.
For instance a player can walk up to the front of a house or chair and will be drawn entirely in front of it. Then he moves to the backside of the house or chair and is partially (or completely) hidden by the object.
This may require a different rendering mode that disregards Tiled's layers, and instead assumes all tiles to be on the same layer with layers for rendering. Then the z order of tiles isn't constricted to a particular layer (the chair would be a problem, because a player character might not be on the same layer as the chair, thus the player would always be either in front of or behind the chair regardless of the y coord).
It was also suggested to have a custom z order per tile, but Tiled doesn't allow properties per tile coord, only properties for each tile. So that probably won't help, but technically it would be trivial to implement in the renderer. So perhaps we need to consider the idea of having a separate (non-visible) z order layer whose only use is to flag tiles that should "move one layer up/down" based on a reference node's y coord.
Okay, clearly this needs more thought put into it. :)
The request should be clear but the (best) solution isn't. Not yet.
Estimate: 5 days, due to likely adding a new rendering mode and additional testing.