VLC media player has two options to show video in fullscreen. The first is called "fullscreen mode" F11 shortcut and the second is "fullscreen" with "f" shortcut.
Both modes appear the same, but the F11 mode make vlc use more CPU and makes Xorg also use about 20% cpu whereas in the other "f" mode, it uses less cpu for VLC and less than 1% for Xorg.
However, using "f" mode doesn't not allow any window to be on top of it. So for example when I activate another window using Xdotool the window is activated as I can see using getactivatewindow but what I can see in the screen is VLC in fullscreen rather than that window. This doesn't happen for "F11" mode but I don't want to use this mode because it uses more CPU power.
I'm using VLC latest version 3.0.8 and I'm running Raspberry pi 3 with Raspbian latest version.