It must mean something different from what I'd thought: this user joined today and has never asked or answered anything, and has 1 reputation. However, this question has a comment by the same user. But the privileges page says the "comment everywhere" privilege is only available to users who have 50 rep or more. Am I misunderstanding the meaning of "comment everywhere"?
No, your understanding is correct. The comment was originally posted as an answer and was converted to a comment by me (something that can be done by any mod).
The comment is an answer transformed in a comment; this is also reported from the comment left from who did it (waiwai933).