These sorts of problems were common in the days before people had access to modern 3D hardware. They occur when you try to fake 3D using 2D overlay techniques. Some configurations are difficult, if not impossible, to represent as simple stacked 2D representations without breaking them up into smaller pieces. However, most people these days tend to use 3D techniques if on a platform that supports them, even if it is only as far as mapping their 2D tiles onto 3D impostor geometry in order to take advantage of the depth buffer for proper drawing. If your tiles have an actual 3D presence that at least roughly conforms to the shape that it could be, it solves a lot of sticky overlap problems.
gamedev.net used to have an Isometric and Tile-based Games sub-forum, but it is now defunct, given that a lot of these older techniques are basically obsolete now. All of the old Isometric posts were folded into the game programming forum. Additionally, some time back I talked more about using a 3D basis here.