I think the biggest change we made that caught us completely unprepared, was that we've committed ourselves to doing the same thing 8 hours a day, 5 days a week, all year long, for decades. I don't think our bodies evolved for this kind of effort (and I use the word "effort" even when the activity requires a lot of sitting, which is appropriate as the article shows).
If you look at hunter-gatherer societies, their activity is more "bursty", more casual. They go gather stuff for a couple hours, then rest; then perhaps do something else. They go hunt something, which is harder, and then rest a longer time. Etc. There might be periods of intense activity, then longer times of rest, or diminished effort. There are also seasonal variations.
The executive functions behind our foreheads, with their long term planning and their delayed gratification, are really pushing us pretty hard in directions that we're not fully adapted to.
Perhaps something similar happened to our diet. Three meals a day, every day, for decades - that's a very recent change in diet. It used to be a lot more "lumpy" throughout the whole evolutionary past that has shaped us.