Sorry to revive an old thread, but since I'm currently playing Majora's Mask, I wanted to add my thoughts.
I don't agree with the dying multiverses, or the clones overlapping. It's the same, one Link, who goes back in time. In Ocarina, he jumps forward and back, but the timeline seems to be flowing forward all the time. In MM, Link has the notebook to help himself keep a record of the many things he can do during those three days. He can choose to do some, and go back to time, and it's like he never did anything. I mean, you always have to defeat the bosses to get some effect, like spring in the mountains. The temples go back to being locked, the fairies are broken, the bosses were technically never killed.
So, what's up with that? Well, I believe that, since Link remains the same, he carries with him the effect/result of his actions. Are the giants really free after you go back in time? I don't think so, but the Oath to Order -forces- them to come back, even if they're not really free. It's a stronger magic than that which keeps them trapped, so to say.
There's no right or wrong, really, just my two cents.