>He uses knowledge from the agricultural industry instead of the "organic" approach.
I can't help but wonder if his knowledge applies specifically to cases where chemicals like fungicide are used. There are quite a few species of soil fungus that are beneficial to plants, including root protection, but these can be wiped out by fungicides, leaving a blank slate for harmful fungus and other pests to take hold. So it would make sense that if there were no beneficial fungus present, then organic matter would be a rot threat.
This conversation is simply more evidence that we conflate meadow/prairie plant behavior with woodland plant behavior. Since permaculturists are generally growing bushes and trees common to successional forest biomes, to an extent both can be right. The expected ratios of nitrogen in these two biomes and the ratios of fungi to bacteria differ by at least an order of magnitude, so of course strategies should differ as well.
With the exception of orchardists (whom some of us think doing everything wrong that you possibly can), modern agriculture concerns itself with prairie plants. Where natural woodland fauna can and do mix decaying logs into the soil column, in a prairie it will mostly be decaying roots (and especially decaying root hairs). The kind of rot going on is a bit different.
That said, saprophytic fungi are generally held to leave living tissues alone. There are exceptions of course, but having decaying woody matter in the soil is not a death sentence.
I can't help but wonder if his knowledge applies specifically to cases where chemicals like fungicide are used. There are quite a few species of soil fungus that are beneficial to plants, including root protection, but these can be wiped out by fungicides, leaving a blank slate for harmful fungus and other pests to take hold. So it would make sense that if there were no beneficial fungus present, then organic matter would be a rot threat.