They are one and the same, because when you are interacting with a window you are actually interacting with controls inside the window. It is easy to forward cursor events to the target window (hover and scroll already do this, FWIW) but when you want to say type something you'll need to focus the text element under the cursor before you can just blast key events to that application.
Doing this in a way that feels intuitive is non-trivial. If you go the simple route and focus every control (so you can do things like tab between them) you run into the issue of the mouse activating some of them as you go over the element and giving it focus–for example, if you do it on a window sidebar, you'll switch between the tabs. I didn't get a chance to really thing about it, but I was thinking of just giving text elements focus and considering it to be good enough; but there are still challenges there: should you be able to focus on a search field (which might blow away the current context and replace it with a "searching" screen)? How should I handle keyboard shortcuts?