Without official response telling us the real motive, I'll share my own opinion, based on my experience on this place, and on Stack Exchange in general.
As I see it, duplicates are special case. They are not off topic like all other close reasons, on the contrary: duplicate question is on topic, and many times a good question on its own.
So it totally deserves a place of its own in the flag/close reason list.
As for why it's also in the "should be closed for another reason" list, couple of reasons:
- Historical: users who are used to find it there won't have to go look for it elsewhere.
- Being the main close reason (e.g. 23 out of 50 recently closed questions on Arqade), having it "featured" in more than one place cause less chance that users will miss it when flagging. Redundancy can be good sometimes.