I have a laptop with a screen that runs on 1366x768 and an external monitor that runs on 1920x1080. When I move the mouse pointer from the laptop onto the external monitor, the pointer comes out on the external monitor in the same height as it does on the laptop. (Pixel to pixel, so the top of the laptop screen is far from the top of the external screen) This is not a big problem, although I probably would expect it to be scaled, somehow. Just in case there is any confusion: the 312 top pixels is a barrier from moving the cursor, 1080-768 = 312.
However, when I move the mouse pointer from the external monitor to the smaller laptop screen, then if the pointer is above the height of the smaller screen, it will stop at the edge. This is annoying by itself, but coupled with features in Gnome Shell, Unity, Unity2D and Compiz (and others) that allow you to maximize vertically by pressing against an edge, this becomes an actual problem.
I think that if I move the pointer horisontally along the upper left of my laptop screen, it should appear at the top of the external screen, as it does at the bottom.
Interesting idea; not sure of the feasibility of implementing it, but will set as a wishlist bug for now.