If there is a window which is out of focus it has the habit of disappearing when the background color matches. The transparency is not your friend here. I have to hunt for the controls to close a window and sometimes, I need to hunt for the window which is obscuring background UI and I need to click on windows to bring them in focus to find their controls.
We need more contrast, maybe the yellow line to show in-focus should always be present, but just not very bright when the window is out of focus.