There is not a “Allow Fall Damage” option on the Mutator Zone Device and there hasn’t been one.
You could using Verse to query for IsFalling from the Players found within the Mutator Zone. If IsFalling returns true, then simply set the Player vulnerability to false with SetVulnerability. Toggle this back to true when leaving the Zone.
I know you mentioned SetVulnerability does not work for your case so perhaps you could try using small Mutator Zones that alter the Gravity Overrides to create an affect where just before the Player lands they are saved by the decreased gravity which may nullify the fall damage