The mitochondria of the two early embryos may have mixed around time of both embryos 'hatching' from the zona pellucida in which they transited to the uterus. HOWEVER, the histocompatibility would be directly related to the membrane formation of stem cells subsequent to the welding of the embryos, since it is the molecular identity complex in the cell membrane that mediates the primary histocompatibility and thus tissue rejection. Somehow (and I have no idea how), the susequent cell membrane formation with stem cells, following the welding of the two embryos inside the chamber formed by a single placental organ, resulted in a cellular membrane combining the histocompatiblity molecules and thus commonality was transmitted to every cell that developed into the birthed organism. [Neat trick, don'tcha know. If scientists could figure out how to do it in a lab setting, tissue rejection that plagues organ transplantation would all but vanish!]