I recently flagged this question as an exact duplicate of this one.

A little later, in my flagging summary I got the message

declined - flags should only be used to make moderators aware of content that requires their intervention

According to this question, I should flag questions that are exact duplicates, but according to the mod who declined my flag, I shouldn't.

Also, if we're not meant to flag them, then why is that even an option in the flagging screen?