Vessel & Body
"My body is Mary's body. Inside of KOS-MOS sleeps Mary's will." - T-elos
The body of Mary, along with the Vessels of Anima, were buried long ago at Rennes-le-Chateau. Before Lost Jersualem's eventual reduction to Planck Scale, Wilhelm recovered the Vessels of Anima. However, for some unknown reason, he was unable to recover Mary's body. It's possible that there was an existance in that place that protected her body for the time being.
Since he was unable to recover Mary's body, T-elos, the body of Mary, could not be created. As a result, KOS-MOS was created as a temporary and completely artificial vessel.
However, the bond Shion and KOS-MOS shared, coupled with the fact that Shion was the reincarnation of the Maiden, lead to Mary's consciousness being awakened within KOS-MOS. After T-elos is defeated and merged with KOS-MOS, Mary awakens completely, though her original memories and characteristics are transformed into a new personality which is both Mary and not Mary. This is similar to Sakura and MOMO.