How do I fix my automatic despawn script?

Well, I recommend not to use Changed as it will trigger if any property of seat changes. The reason why it is still destroying, maybe when you spawn it, the property of seat might change, which trigger the Destroy command. To fix this, just replace Changed with GetPropertyChangedSignal(). It should look like this :

local car = script.Parent
local seat = script.Parent.VehicleSeat

seat:GetPropertyChangedSignal("Occupant"):Connect(function()
	if not seat.Occupant then
		wait(20) 
		if not seat.Occupant then -- Double-check whether the player is sitting or not
			car:Destroy()
		end
	end
end)

-- Now, you were asking why it isn't despawning when you spawn it. It is because the occupant property doesn't change. Here's an example that you can use.
local onSpawn = tick() -- tick() is the number of seconds that have passed from January 1970

wait(20) -- Waits for 20 seconds

if tick() - onSpawn >= 20 and not seat.Occupant then -- If the number of seconds passed is greater than 20 
	if not seat.Occupant then -- If no one sits on it
		car:Destroy() -- Destroys it
	end
end

-- Important : There's no mandatory usage of tick() here. I just added it for educational purposes and double checking the time.

It will trigger whenever the property mentioned in () changes.

Lemme know if it helps!