So while I was showering I started to think, if we connect the Yozora cutscenes to the versus xiii concept, I started to think that Noctis really was supposed to be in kingdom hearts if versus happened. If I remember correctly (and I may screw up some things I don't have a good memory) Noctis in versus was supposed to see the dead because of a near death experience, a gift given to him by the goddess Etro, the goddess of death. If we connect that with the events of kingdom hearts and Sora disappearing, it would make sense for Yozora to see Sora and question the whole thing because he sees this boy in his dream and he can't tell if he's real or not, dead or alive, going by the versus concept.