This is a very good question. Sometimes, a comma is useful to separate ideas or to aid the reader. It doesn't happen very often, and it's really the author's call. In your example, the comma is used to ensure the reader sees the "comment on the sentence" as one element. The phrase "not part of it" is an adverbial phrase modifying "is". (It is possible to separate adverbial phrases from the rest of the sentence with a comma, especially ones at the start of a sentence.)