I've had this problem for a long time on my mac, but decided to post just now
After the playback starts the pointer hides after the delay (according to settings), but after a second or maybe the exact same delay it reappears and stays on top of the video. Which is quite irritating, have to place somewhere in the upper corner (trying not to trigger active mac os x corners) and pretent it's not there.
Mac OS X 10.14. VLC 3.0.8.
But the problem persisted through many versions it seems.
Would be grateful for any help. Thanks!