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When you use the 3D functionality, there are a number of other things that can no longer be used.
You cannot use background and foregrounds in your rooms anymore. (The reason is that they are tiled to fill the image but with perspective projections this no longer work correctly).
You cannot use the mouse position anymore. The mouse will not be transformed to the 3D coordinates. You can still get the position of the mouse on the screen (in the view) but you will have to do calculation with this yourself (or not use the mouse at all).
You cannot use tiles anymore. Tiles will most likely no longer match up correctly.
Collision checking still uses the 2-d positions of the instances in the room. So there is no collision detection in 3D. Sometimes you can still use this (if you use the room as a representation of a flat world (e.g. for racing or FPS games) but in other situations you have to do things yourself.