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.

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."