The studies are pretty clear: aerobic exercise leads to some tepid reduction in body fat in exchange for massive effort, and resistance training increases fat-free mass but doesn't reduce fat.
> [aligned] with literature from the previous decade and recent systematic reviews concluding that participation in an exercise training program does favor weight loss, although of only modest magnitude. [1]
> Resistance training was the only exercise modality that failed to significantly decrease visceral adipose tissue. [1]
You suggest that "you'd much rather someone be a muscular, overweight person than skinny-fat person" -- but that's not really the case. Sheer fat mass, especially visceral adipose tissue, is what is associated with negative health consequences.
[edit] Even the article you linked to via the Times says the following.
> However, the amount of weight loss from exercise training is often disappointingly less than expected. [2]
Which aligns with their own findings that after 12 weeks of 3000kcal/week energy deficit they only lost about 5 pounds, see Table 2. So to lose 50 pounds you'd have to spend 2 years with a 3000kcal/week deficit, and keep adjusting periodically. The chances of compliance here are literally zero, and compliance is a major issue. In some senses, it's the major issue.
Also this study committed a major sin: they didn't follow up. Any study that shows anything meaningful in re: weight loss reverses after 6 months.
[1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8365736/
[2] https://journals.physiology.org/doi/full/10.1152/ajpregu.000...