We could do better with the fading, but I find myself unable to imagine
a situation where someone simultaneously (a) needs to see what's under a
notification bubble and (b) "needs the cursor elsewhere". Can you give
an example?
I think Michael Jonker already provided one at this very thread; that's why I elaborated on it. When working with the Gimp, he needed to see the layers panel while working on the scene, and it was obscured by the bubble.
This will happen in general whenever the top-right corner of the application contains an information panel, which is intended to contain readable data that can be read with a glance while working on the main interface. This is quite usual in IDEs and design tools.