I do the same thing as the author. If I see that the comment stream is somehow related to my FB account, I skip commenting. I don't know how they're used or how they feed into some other FB stream.

Even if I did have a feel for how those comments currently are integrated with other FB comment streams, none of us has any idea of how FB will change their policies in the future that will totally wreck our personal notions of "separation of concerns".

Well the three reasons that the author is hating on FB comments are bulleted in his 16 sentence blog post, so it should be relatively easy to figure out why he is hating FB comments.

Your counterpoint only addresses the first of his three reasons.