First, interesting column.
Second, a point that could perhaps improve the article: the whole analysis of energy is suspect (and I find it very odd the military would use such an inaccurate predictor of physical damage). Energy is only indirectly related to the damage a bullet can do.
What really matters is how concentrated that energy is. I have a sharp knife in my kitchen. I also have an ice-cream scoop that has about twice the mass of the knife. I can hit my hand hard with the scoop, and it stings, but does no lasting damage. I can hit it with the back of the knife, and again it hurts, but doesn’t damage. If I hit with the blade, I could easily cut myself badly.
Clearly, the scoop (which hits with more kinetic energy) is ineffective at causing damage, while the blade of the knife (which had equal kinetic energy to the back of the knife, and less kinetic energy than the scoop) is very effective at causing damage. So energy only tells part of the story.
What also matters is how focused the energy is. We cut with the sharp end of the knife not because it provides more energy than the back (it provides the same, speed of the blade being equal). We cut with the sharp end because it focuses the energy into a very small area – this causes the stresses just underneath the knife to be very, very high (stress = force/area, so small area => big stress). So the area directly under the blade is damaged by the high stress, and fails, and the blade moves deeper into the object, stressing the area just below the original (now-cut area), and this keeps on as long as there is adequate energy left.
That being said, it is clear that whether a bullet falls point-up or point-down is of great importance. A point-down bullet will concentrate the energy much greater, and has a much better chance of piercing the skull. Further, a point-down bullet will be more aerodynamic, thus have a higher terminal velocity so it will strike with more energy than the point-up bullet. Again, though, it isn’t truly the total energy that determines how much damage an object can inflict, but rather the concentration of energy at the point of impact.