The AO ghosting of invisible objects issue is (almost) solved in 3.9 pre 1!
However, there is still a slight AO ghosting visible of completely transparent objects even if object visibility is keyed in the timeline.
Only if the object is hidden using puzzles the AO ghosting fully disappears.
I tried to hide an object if it is on a certain key-frame with puzzles but that didn’t work. It would also be a hassle to implement in complex animations.
Hopefully, you will find a way to make Keyed Object Visibility export to Verge3D or make the AO for transparent objects completely invisible.