So, here's how I understand it. Yes, Vanitas is using a replica body so that his heart from the past can exist in the present. However, it seems to me that each of the hearts of the Organization members brought into replica bodies from the past were taken at the point of their initial destruction. Ansem and Xemnas, for instance, would have been picked up by Young Xehanort immediately after or at the point of their demise and brought forward in time. Now, we have to remember what happened to Vanitas in BBS. After the clash with Ventus in their shared Station of Awakening, both Ventus' and Vanitas' hearts became fractured. Ventus managed to rescue his heart by hibernating inside of Sora's, the person who had made him whole to begin with. Vanitas, on the other hand, after being brought forward in time by YX, would have used the screams and negative emotions from Monstropolis to restructure his own heart in the same way.