No, unless you change the alignment of your screens (System settings > "screens", drag the left screen up), but then you would have the same problem at the bottom.
In Unity (/Compiz), both screens together are seen as one big desktop/viewport. From that point of view, it would be undesirable behavior as well; the mouse would either make a weird jump down, or disappear to nowhere, and be invisible unless you move it down.
The first option would be inconsistent behavior in combination with possible windows, spread over two screens, the disadvantage of second option needs no further explanation I guess.
Like everything in computer life, it can be scripted, but again, I would not want that, for the reasons above.
From your comments, I understand that you feel the mouse should (on transition) move to a vertical position, relatively equal to the position on the screen it came from. That is exactly the misunderstanding, since windows (and anything else on the desktop) have an absolute size and position (in px). Windows can even be spread over two screens. You can not combine those two and have a consistent desktop.