The concept of a damaged metabolism doesn't make sense. Your body doesn't waste energy for the hell of it, there is not even a dial for the metabolism to change. Your organs just perform their functions using energy in the process. An organ can't reduce its energy expenditure without compromising its function. Not to mention that if it were possible to live with less calories, evolution would have eked out that benefit millions of years ago.
It is well known that the resting energy expenditure is a simple function of body composition, with no influence of age, gender or body weight [0]
The first study attributes the drop in energy expenditure to the non-resting energy expenditure, which isn't part of the metabolism. There is no saying that difference in energy expenditure isn't compensated for in real life situations, the study freely admits the difficulty in controlling for it.
The second study shows a drop of energy expenditure of a whopping 2%. Another explanation of the effect could just be that the formula they use to predict the resting metabolic rate is too simple, it literally only uses two variables: fat mass and fat free mass. You wouldn't expect such a simple formula to hold over a wide range of weights, it's surprising that it works so well, to within 2%, in the first place.
The third one, the Biggest Loser study, is the only one of the three that is just plain wrong. I'm very surprised to see it appear on Scientific American. In the study, they invent their own formula for the RMR by doing a multilinear regression in 4 variables on 14 subjects. This formula is different from the usual formulae and tellingly underestimates the caloric need of fat tissue (1.5 kcal/d/kg instead of 3.5 kcal/d/kg or 5.7 kcal/d/kg as in your second study). Then they apply that formula, which was calibrated only on the obese subjects, on the people after they lost weight and compare that to the measured RMR, instead of using a more standard formula, and interpret the difference as metabolic damage. No wonder it doesn't work. If you instead plug in the data in a more accepted formula, you see little difference with the measured metabolic rate. Heck, even I have massive metabolic damage according to that formula, their formula estimates my RMR at a whopping 2460 kcal/d, which isn't my total daily energy expenditure. The measured RMR in the article, 1903 kcal/d, wouldn't be unusual for people of that weight.
That study should have never gotten past peer review, and I don't know why it hasn't been retracted yet.
I don't understand the focus on metabolism anyway. Even if a damaged metabolism existed (it doesn't), that still wouldn't change anything if you ate less. The problem lies in a miscalibration between satiation and energy need, we should be figuring out why some people are more hungry than others, and what we can do to change that.
0: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3139779/