Welll, maybe think of it like this: The clone Sakura and Sakura-hime "technically" had the samle soul to start but, as time when on and they each experienced different things, thye became their own person. I think that reincarnations and clones/doubles simply have souls VERY VERY close to one another, but there are small differences that make them unique and individual at the same time.

And I honestly don't know which pair I ship more: Kobato/Fujimoto or Yorogi/Shuisho XD