The trouble with biodiversity isn't about lower yield-per-acre, but more that it's not the most affordably scalable. It's not hard to set up and configure planting a homogeneous crop across a vast range of acreage, then hit each stage of the process (fertilizing, weed-killing, harvesting) with vastly powerful equipment in what's effectively an array. It takes more work to create an interdependent system that uses nature to fix nature, but many communities have done it for centuries (e.g., the Mennonites).
The one risk of scaling is that it's a short-term gain with a specific technical debt with the soil: too many repeat seasons of the same monoculture will create weaker yields from the decreased essential minerals for that specific plant. There are a host of existing solutions to this, with varying degrees of implementation and effectiveness:
1. Plant different monocultures in that location each year, though this isn't so useful if the entire region is configured for a particular plant. Iowa may be better for corn and Kansas for wheat, for example, meaning the market yield will be diminished for functionally the same product.
2. Employ the ancient method of "letting it rest" by not planting it every 7th year or so. Cuts back on profits, but lets the land heal from simple non-use (e.g., bugs and birds do their thing). The article implies this one, but with strips of rainforest in the middle of the acreage.
3. Rotational farming with grass seed and ruminants. Roaming cattle are literally the answer to climate stability, for multiple reasons.
As it stands, farming at scale works that way because it's been the cheapest way to get the most crops. There are only several ways to improve food availability:
1. selective breeding and (now) gene-splicing, which makes the food more resistant to damage, larger, sweeter, etc. at the cost of quality
2. government incentives for "good old-fashioned non-GMO organic produce", since most people will not pay an additional $1/lb for apples
The trouble with the article is that it abides by what I call the "Fragile Earth Theory", which posits that any aberrant act by humanity could send the entire planet into a downward spiral that renders us all extinct. There's enough scientific evidence to disprove that idea, but it's not politically fashionable to argue it and not the hill I want to die on. The article is interesting regarding biodiversity, but food security is now more a political issue than a yield issue.