window-x11: Fix the coordinates we use in the synthetic ConfigureNotify

Before, we were using the root window coordinates of the client window,
rather than the toplevel frame window. This caused various Java programs
and programs like VirtualBox and WINE to get confused about where their
window actually is, and make bad ConfigureRequests when trying to
position their windows in the future.

Remove the mass of code here by just using window->rect.