Check your cursor settings. Youtube has their own on screen controls.

I know how to shorten it, but you might need to experiment a little bit with the timing. Here's how:

(1) In a new tab, type or paste about:config in the address bar and press Enter/Return. Click the button accepting the risk.

More info on about:config: Configuration Editor for Firefox. The moderators would like us to remind you that changes made through this back door aren't fully supported and aren't guaranteed to continue working in the future.

(2) In the search box in the page, type or paste full-screen-api.warning and pause while the list is filtered. Firefox should show two preferences.

(3) Double-click the full-screen-api.warning.delay preference to display an editing field, and change the value to 0 then press Enter or click the blue check mark button to save the change.

(4) Double-click the full-screen-api.warning.timeout preference to display an editing field, and change the value to 0 then press Enter or click the blue check mark button to save the change.

In another tab, test how it works. If you get the full 3-second warning, try increasing those values from zero and zero to 5 and 5 and test again. Tweak until you find the best values.

Success?

I just realized you already have that part sorted and you are referring to moving the mouse pointer to the top of the screen. I don't think there is a setting to suppress that. Possibly there is a custom CSS hack.