Mike,
Some thoughts:
1. I think you would find that many flies actually end up riding upside down in a fashion similar to clousers.
2. I'm not sure of your source's training in fish neuroanatomy. Fish hooked in the upper section of the mouth are rarely hooked deeply in that spot. It's usually a very horizontal hookset at 5-10 degree angles to the roof of the mouth.
3. If you and other anglers were consistently "gouging the brain pan" of schoolies, they probably would not swim away.(at least not in a straight line)
4. Flies withought metal dumbell eyes often end up in the gills or cause bleeding in the area. This blood loss can be excessive or lead to infection. Gill damage may cause more damage to fish than roof of the mouth/brain injuries.
5. As much as we all love it, it's not a gentle sport. One must come to terms with the fact that some fish, although released, may die due to a variety of angling stresses.
Dave