It is measured from the outside bottom of the trailer box to the top. If there is a bow in the roof or a roof vent, A/C, etc., this is NOT included in the measurement.
If you need the highest point of your trailer to be no more than a specific height, make sure to allow for the previous mentioned items when you calculate the height requirement of your trailer.
Also, make sure you explain this very clearly on your written order so that your dealer is aware.
Many buyers like to keep their trailer in their garage and only have a certain amount of clearance height. It is only when they are unable to get it into their garage that they realize the height miscalculation.
