If your that concerned about the time for any water to re settle just try a little experiment with a small jar full of fuel, add a little water and then stir like crazy. See how long it takes to settle out.
It doesnt take that long!!!! How long do you wait after re-fuelling before doing a water drain??? I bet not an hour.
As for drain points being at the lowest point of the system, this is generally true, but as I mentioned before there are a number of aircraft with rubber bladder style fuel tanks which over time begin to resemble a deflated ballon with all the associated ripples, water can collect in these ripples and it doesnt matter where youre fuel drain is it will never get to it...