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 their kids because the mother can't carry many infants with her, but settled people don't have that problem, their women could (and did) pop out children every year and basically overwhelmed the nomads. Though what you are saying about the food surplus allowing luxuries like specialized craftsmen, research, etc. is certainly true as well.

you can indeed have a vegan diet, and avoid all or nearly all of the issues the article cites

One can, but doesn't mean that all vegans do.