Disclaimer I am not a medical scientist: but I'd like to understand more about how they found the participants. It strikes me that people who perform meditation might be different than whatever controls they were able to find. The fact they re-used participants from previous studies also strikes me as worrying.
Preferably they would take participants at random and have half perform the meditation for (12 or 24 months) and look for changes. Using self-selection might be more difficult to prove causation.
The book Altered Traits goes over a lot of the scientific results, I think it's two chapters of the book that cover this stuff. One of the studies they cover studied people who had never meditated, people with 10,000 hours and people with about 36,000 hours of meditation if I recall correctly. This last group is the one that exhibited altered traits, and it's not easy to find people with this many hours of practice, hence why they reuse the participants. All other participants exhibited some of the altered traits but only during intense meditation periods, the master meditators exhibited them all the time.
The results from the book are/study are hard to interpret, something about sustaining gamma waves for long periods of time and having younger brains in those that practiced meditation a lot. They also recovered from pain faster, and wouldn't develop anxieties about it.
Since these subjects are very interesting, it makes sense to study them again with different techniques or reproducing previous results.
> it's not easy to find people with this many hours of practice, hence why they reuse the participants [...]. Since these subjects are very interesting, it makes sense to study them again with different techniques or reproducing previous results.
That's fine as far as it goes. It helps us confirm that a phenomenon can actually occur and perhaps tells us something about its general shape. But when studying a population of known outliers, it's not credible to assume how the results will or won't apply to a broader population. This isn't an abstract epistemological concern; scientific journals are absolutely packed with exciting preliminary findings that vanished into insignificance when somebody did a larger or more rigorous study (but nevertheless might be cherry-picked for a pop-science/self-help book based on the "revolutionary" findings).
Judging from the age range (and from a previous life as a neuroscientist) they're probably undergrad and grad students who signed up because they saw an advert on a college notice board and thought it would be cool to have a brain scan. There's big issue in recruitment of subjects where many, many studies use WEIRD people as subjects - Western, Educated, and from Industrialized, Rich, and Democratic countries. It costs a hell of a lot more if you want to recruit a broad section of subjects. I'm not sure that participant re-use would be a big issue here because it's an anatomical study, unlike other studies where subjects might have learned skills from previous rounds of testing.
However, they do say in this paper that "Control subjects had no previous experience with meditation or similar practices." They're careful not to make claims in the paper that the mediation caused the changes in brain structure - "our findings suggest that long-term meditators have structural differences in both gray and white matter" - which point to exactly what you were suggesting as a next step: take a group of people who've never meditated before, split them into a meditation and non-mediation group and follow up after a year or two.
Preferably they would take participants at random and have half perform the meditation for (12 or 24 months) and look for changes. Using self-selection might be more difficult to prove causation.