To me it seems the top menu bar is a holdover from early Mac OS. I saw a demo of one of the early versions of the OS, and it made a ton of sense there. The OS could only run a single application at a time, but that application could have multiple windows. From that perspective it's very sensible that whichever application had full control over the screen would want a menu bar global to its own windows.
Now though, it's just weird to have the menu bar at the top of the screen. And it's especially strange when there's no windows for the application left but the menu bar for it is still visible (something that wouldn't be strange in the single app at a time model)