Another hypothesis would be that agriculture and civilization allowed a larger number of smaller individuals to survive. Modern humans tend to increase in size if they have a better diet, especially in childhood.
Civilization and the attendant agriculture brought a primarily grain-based diet to humans who earlier lived off a varied diet that included a lot of animal protein and better nutritional balance. Hard to imagine that would not have impacted intellectual development. After all wolves are quite a bit smarter than domesticated dogs on average.