GUI on top instead of video
As the name video-on-top
and description ("Always place the video window on top of other windows."), the always-on-top setting is for the video window.
The Qt GUI is a bit too eager to go on top of everything, as it goes on top even when there is no video, or when the video is not embedded in the GUI. This notably causes the GUI to go on top of the video, which very much misses the point...