This bug is still present and it's in the player itself.
I did a full uninstall, cleared all registry entries, tried multiple versions including 3.0.0 and yet the box "Above the video" still does zilch, nothing.
After retrieving the interface settings from an old install of VLC 2.1.1, I seem to have found the problem and have a fix for anyone finding this thread:
- Navigate to C:\Users\Your Name\AppData\Roaming\vlc or simply press Win+R and enter %AppData%\Roaming\vlc to get there quickly.
- Open vlc-qt-interface.ini with a text editor of your choice.
- Change ToolbarPos=True to ToolbarPos=1.
- Save the file.
There you go, the toolbar is above the video again.
Now any change you'll make in interface settings will revert this value, so you'll have to change it to "1" again, after you've set everything else to your liking.
Hope this may be fixed now.