The procedure is terminated quickly once the person is entering distress due to lack of oxygen.
The first few times it's done on a person, it's very frightening. Later, it becomes very annoying, especially if they wake you up at 4 AM for another go.
You make it sound like the DoD, Amnesty International and the Red Cross had a couple of meetings on this and came up with a humane way of doing this.
if you're interested in hammering out some science for us, waterboard yourself and report back. i think you might be surprised.
That being said getting a good scan required me lying on my back holding still as I was slowly lowered into the water. At the end of the scan I had water going into my nose. Holding my breath was unable to prevent this. Certainly not as bad as waterboarding, but certainly enough to elicit a coughing fit.