I can alt-click a window to move it in Xfree even if the application is blocking and I happen to click on a portion of the window that the application itself is responsible for drawing.
So even though the application is drawing the main body I can still move it around by alt-clicking on the main body and dragging it even if the window is unresponsive.
So this does not seem to be a significant problem at all. All Wayland has to do is be aware of the what is the 'title bar' region of the window and be able to act accordingly when you click on that portion. It doesn't have to draw the title bar or close buttons to be aware of the them and be able to respond to clicks in the area of those items independently of the application itself.