The article supports that agricultural diets were worse - but the hunter-gatherers were, as well. Nobody ate a lot back then, abundance is fairly new to humanity. The important part about agriculture is not that it might be healthier - far from it.
Agriculture (and the agricultural diets that go with it) allowed humanity luxuries that the hunter-gatherer did not have - a dependable food supply, and moreover a supply where a person could grow more food than they actually needed for subsistence. This is the very foundation of civilization, and all of the benefits derived from that - the freed up workers could spend their time on other things like permanent structures, research into new technologies, trade, exploration, that were simply impossible in hunter-gatherer society. You can afford to be sickish, as a society, if you can have more babies and support a higher population, at least temporarily. (I suspect that beyond this, adapting to the diet was probably a big issue, and continues to be - look at how many are still lactose intolerant...)
Over time, that allowed agrarian culture to become far better nourished - to the point where sheer abundance causes a whole new set of health issues. I would suggest that today the issues with diet are those of abundance, not agricultural versus hunter-gatherer types of food choices. And, today, with the information we have - you can indeed have a vegan diet, and avoid all or nearly all of the issues the article cites. Technology rocks.
Nobody ate a lot back then
I don't think this is true. Contemporary hunter-gatherers leading traditional lifestyles are not malnourished or permanently hungry. They certainly have problems (like the parasite load or an occasional famine), but I have a strong impression that their quality and amount of food is fine.
allowed humanity luxuries that the hunter-gatherer did not have
Yes, of course -- the agriculture people did win and take over the world :-) My understanding is that the primary way they won was through breeding faster: nomads have to space...
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