That sounds like a problem with the definition of overweight, which probably uses BMI. BMI doesn't seem to scale well to athletic builds.
For the biggest group of American men, this article is implying that they are unhealthy, when the facts are that they are actually healthy.
I'm not saying this isn't among the most important health issues in the US. I just think you need a more reasonable standard or a lot of people will just throw up their hands.
The BMI of athletes, or the limited options of people who live in food deserts, really seem like missing-the-forest-for-the-trees tangents in these sorts of discussions. According to the "rise of obesity in America" chart in the article, overweight-or-more among American women went from about 40% in 1960 to about 80% in 2014, with the highest percentage increase in the "extremely obese" subgroup. It's interesting to speculate about what drives it. But I don't think we can explain the trend with "they got shredded" or "they moved to food deserts" when we're talking about 40% of all American women.
Maybe my intuition is wrong -- maybe there are enough people with high muscle mass that it's skewing entire charts like the Vox article shows. If you have citations to that effect, I'll read them with gratitude.