Unsurprisingly, the title is sensationalist and not representative of the study. The study compares energy expenditure across different economic groups i.e. western people sitting in offices versus hunter-gatherers in Africa, and found that difference in energy expenditure does not account for differences in obesity, so points to consumption as the likely reason. The sample dataset explicitly excluded 'athletes', so…
Obviously, energy has to come from somewhere, so enough exercise will overcome any adaptations your body makes, but the current evidence seems to suggest that there is a lot of wiggle room for your body to cut energy expenditure to make up for any exercising you do. The evidence suggests this takes time, but it does also suggest that the 20 minutes on the bike daily that helped you drop some pounds at the start will not do much for your weight a year in.
I don't know if it's true or not, but when I first read one of the studies, it did make some intuitive sense to me - humans have spent much of their evolutionary history having to expend significant energy to procure food. If you had to walk 30,000 steps in a day to forage or hunt, it makes sense that limiting other movements while idle, etc., to help preserve energy stores would be beneficial.