Isn't this obvious? I mean if you need that kind of control of the screen then you shouldn't be working inside a WM by definition, and the Toolkits are built for building interfaces in the context of WMs. Right? I definitely don't want your random application to be able to draw on arbitrary parts of the screen and then prevent anyone else from drawing over it. Your use-case might sound simple at first glance, but it's truly odd if you think about how I interact with applications, and how I expect to be able to manage them.
Of course. I'm not saying that using Win32 or Cocoa are wrong (at least for a Desktop OS where you don't want to hand over full control to an app), just that they're closer on the spectrum to Qt than bare metal.