> Manure isn't a problem if you free range your animals, have landscape structures to prevent runoff and have other animals that eat bugs in the same space such as chickens. Then it just contributes fertility to the land.
I would contest that. Animal manure runoff has always been a problem to e.g. brooks and rivers and only in recent years has the legislation started to prevent some of the more problematic practices. Like grazing all your cattle on a soon-to-be-flooded grassland next to the river. Nitrate pollution of the ground water is also more pronounced in German areas where free-range animals are more common.
> Industrial farming is stupid, and totally unnecessary. Using permaculture and silvopasture, you can produce much more (and more nutritious) food in the same space, while improving (rather than destroying) fertility. If done right, you don't need pesticides, your animals don't need antibiotics or dewormers, and the whole thing mostly runs itself aside from a little pruning/herding and a lot of picking. The only downside to these methods is they take some time to get going, and they require knowledgeable farm workers rather than dirt cheap migrant laborers or a combine.
If it were only farmer's knowledge that is required, farming industry would do it in an instant, considering the significant advantages you named.
I would guess that either the methods you mention are far more labour-intensive as well as requiring more qualified labour. Or that the advantages aren't really that significant. Industrial agriculture is hunting for every bit of efficiency gain, and lots of businesses are looking for an edge any way they can. So it seems strange to me that the methods you mention aren't used in any significant amount.