There are a lot of reasons why smaller farms produce more per unit area than larger farmers. One is because of the more complex systems, as I explained. Small farmers also benefit by integrating crops and livestock. So there's recycling of nutrients and biomass within the system. That also makes it more efficient and productive.
Small farmers tend to invest more labor in their land.
That too makes it more productive. And the quality of the labor is much better. When it's a farm family whose future depends upon maintaining the productivity of that soil and that piece of land, they naturally take better care of it. When it's a huge corporate farm with relatively alienated wage labor doing the work, the employees do not have the kind of tie to the future of that piece of land that they would if they were family farmers. It seems as if some of these benefits are not necessarily inherent in size but just in the different styles of farming.