Thanks for the write-up. This same problem was discussed frequently by James C. Scott in his book Seeing Like A State. He ascribed soil depletion to narrow-minded optimization techniques that sought to maximize one or two variables (eg. yield per acre.)
Turns out that the purportedly disorganized Third World farmers who farmed the old-fashioned way (eg. multicrop) were better maintainers of the soil than the purportedly efficient factory-style farmers.