Our moderation team works very hard, each active moderator on the site spends an average of at least an hour a day, if not more, looking at the worst content that we have to offer. At an average of almost 2,000 flags per day, we ask a lot of these folks - and they consistently give us more than we ask for when it comes to their time and patience.
You were, as others pointed out, notified that the type of flag you were raising was not necessary - the system automatically raises those flags. It's likely that you didn't notice the first flag rejected, and continued to keep flagging.
Moderators declining a flag have a very limited number of characters to enter if they wish to give a custom response, and he was trying to point out to you that you were wasting your time by raising the flags. While it came off somewhat snarky, he was trying to be helpful. He's also human. Comments, chat and possibly a system sent moderator message might have been a better way to reach you, but hindsight is always crystal clear.
To answer your question again, directly - while we appreciate your time, the system automatically flags duplicate content by the same author, so no, you don't need to flag it.
If you see duplicate content by different authors flag it, we're probably dealing with plagiarism which is a very serious issue, one the moderator you interacted with is very good at investigating and ultimately handling :) The system really can't, therefore doesn't automatically raise flags for this.