It didn't really go into detail about what parts have shrunk. It may be the primitive sides.
With the advent of growing size, I think it may be the parts set in motion by do-no-think-yourself religiousness. That certainly had its time in the sun.
On an earlier scale with a growing society you don't need each and every one to fend for themselves alone, otoh that allows specialization.
But there has been a need for leaders to help development, and I think those have been found among the people who are naturally able, but not aggressive.
Aggression is something that solves itself, if there is no longer a need, there is no longer a climate for aggression. That is however looking at the bigger picture, and not accounting for automated, and especially nuclear weapons.
Devastating losses on both sides is something new to modern warfare I think, but it pans out with civilian losses.
If you subscribe to the theory that we are all just carriers of our genes, and act on behalf of them, we are in for interesting times. How long since your genes were put to the test on such a broad front? Just about everything changes. Wielding an axe used to be lots of professions, today its only semi-useful at best.
Edit: The wiki link (which i didnt check sources to) seemed to rule out nutritional value, and at the same time acknowledge it. If the people born after the time of crisis truly are smarter, couldn't this all be down to biological effect of crisis on parents, both before and after?
Also I seem to remember seeing something about first-borns being intellectually superior to their later born siblings, that would describe difference in the situation in densely populated modern areas vs agricultural rural areas quite well.
Observationally elder siblings are mentally different from their younger brothers and sisters, but its kinda easy to say that while they are for the most part growing up in the same household at the same time.
Guess we need a control-group of siblings adopted into similar homes in similar environments. That, or you stir the pot long enough to develop some clues that can reliably predict the future.