The biggest issue with this study (other than being a sample of 1), is they took someone who started in much better condition than most people are at. He could only remain at the same level or experience a decrease like he did. There was no possible upside in his case. It would have been more relevant to most thru-hikers, if they had taken a person who was more typical and see how their body changed.
Here is another study with a sample of 1 for a month long hike of the Colorado trail. The body changes aren't going to be the same as a 4-5 month hike so it's not comparing the same thing, but it gives a more expected result, though it's emphasizing a different aspect of health than the OP study.
That said, the poor diet of most thru-hikers is well known and must have some negative effect. While some make an attempt to maintain some amount of nutrition, but most are happy that they are loosing weight while having the food preferences of a child. It's really telling to see how most thru-hikers eat when they get to town and now have access to healthier choices but refuse to take advantage of it. I'm not against having pizza in town, but not every night, and I do like to get some green salads and plenty of veggies to go with whatever I'm having.
When I hiked the PCT, I made an effort to make better choices and not live on just overly processed food (though I still had my daily snickers), and somehow only lost 10 pounds by the end despite wishing I had lost another 10-15 pounds as I still had plenty of body fat despite doing 24-27 mpd for most of the hike. I don't think I was carrying a lot more food weight than most hikers. The idea that a calorie from one source is the same as one from another is a myth. Your body needs other things to make full use of those calories and keep your body healthy.