Though not explicitly written in the article, it seemed to me that JJ was recommending this approach for dealing with short-lived 'topic' branches like bug fixes and small features. At least, that was the nature of each example branch he gave.

I agree with you that if you have a longer-lived branch that's shared among repositories, you'll want to see that merge in the history and optionally squash some of the commits as needed. For short lived topic branches, I often like to squash down to a single commit.