I'd argue that the author is criticising cynicism, rather than skepticism. Healthy, genuine skepticism should take into account the amount of scientific attention devoted to a topic.
When I was young I read a book called Bad Thoughts by a philosopher called Jamie Whyte. In hindsight it wasn't a great book, but it did leave me with the memorable phrase "Cynicism, like gullibility, is a symptom of underdeveloped critical faculties."
I would be incredibly surprised if repeated meditation didn't alter brain structure. We have a lot of evidence of other prolonged activities (taxi cab driving, drugs, and others) significantly altering brain structure.