The author is correct: JSON shouldn't be used for configuration files (or for anything else for that matter!), but not because it lacks comments, but because it's very difficult to construct a parser for it. (Just yesterday I had to compile and package jq because writing a parser of my own for it would be insanity).

Configuration should be done with operating system packages and shell scripting; then there is no need for comments, since the files for making the package are kept in a revision control system like Bitkeeper or Mercurial and configuration on systems never modified by a human.