Reminds me of some of the discussion in Charles Mann's "1491", regarding the agricultural techniques of the Indians (honoring his use of that over Native Americans) before the Colombian Exchange [0]. The natives in South America had figured out symbiotic relationships between several plant species and grew them together in "Milpas" [1] (and how this goes against the "pristine land" myth many mistakenly hold regarding the Indian's use of the land).
"Pristine lands" lied far north of there, and were used as pastures and hunting grounds.
Agriculture was practiced in more southern lands, where the yields are higher. Corn comes from the south of North America, and potatoes, from north of South America. I think nobody had a delusion, even back in 1500s, that these were wild plants.
Well the main problem is that population growth means that the traditional farming productivity - while sustainable for millenia - just isn't enough to feed the whole population of Indonesia and Bali in particular. Bali went from 1.5 million in 1945 (independence) to 2.9 million in 1989. The traditional approach is opening up new land but of course you can see how this is unsustainable.
So unfortunately the switch from biannual harvests to triannual harvests using factory-borne fertilizers and deep water usage was necessary.
(I was taught this in a fertilizer factory visit near Surabaya a few years back, so my information might be highly biased. But demographics data is there and ... It is what it is.)
The Subak system demonstrates the Vedic way [0] of life in which the divinity (pure consciousness) is seen in everything – mountains, lakes, rivers, plants, animals – in all species. Temples and regional deities bind together and nourishes the whole ecosystem, preserving the environment and wildlife.
Unfortunately, as evident in the article, blindfolded by the supremacy of material science, the modern society has mostly destroyed this ecosystem without understanding its benefits, and it now wants to prevent climate catastrophe by carbon credits and other commercially driven policies rather than learning the natural and inclusive (spiritual) ways of the olden times.
Never ignore centuries old knowledge, seek to understand it first before trying to use modern methods for agriculture. The article is exactly about the story around understanding why old methods for agriculture worked better than modern ones.
[0]: https://www.penguinrandomhouse.com/books/107178/1491-second-...
[1]: https://en.wikipedia.org/wiki/Milpa