Compatability mode doesn't make a difference. However, have noticed a few more things that may help narrow this down:
-Not be limited to Mojave -- just more visible on my system conected to Mojave
-Problem goes away when I turn off Ambient Mode in Youtube Settings
-Ambient Mode is not visible on my Catalina system when not in Dark Mode (becomes available when I set Youtube's Appearence to Dark Mode)
-On laptop running Catalina with Google's Appearence set to Dark Mode and Ambient Mode left on (the default) and player controls autohidden, I do see flicker though it is somewhat muffled by LCD
Also it may be content dependent (probably because of interaction with Ambient Mode and Dark Mode). Out of three tries, two videos from unrelated sources triggered it and one didn't. This is one that did:
As such what should trigger it is the following combination:
-Dark Mode On (whether as a Mac system setting or a Youtube Appearence override)
-Select video content that oscillates some Ambient Mode related screen adjustment
-Ambient Mode On (default)
-Full Screen
-Player controls allowed to autohide and no other Youtube diagnostics (e.g. Stats for Nerds)
While that seems esoteric that is basically my default viewing mode for Youtube content (i.e. Dark Mode, full-screen, player controls autohide, other settings left to default which leaves Ambient Mode on). I can however easily turn off Ambient Mode as a workaround.
While not limited to Mojave unclear if issue persits past Catalina. Will try Monterey when I get a chance to test further.