My theory about how they are going to reveal the Player's identity without using Live Action humans(cause that wouldn't really fit in my opinion):

At the end of Chapter 5(or whatever Chapter we meet the Prototype in), the Player arrives in the Labs just outside of the Prototype's Boss Room. In order to enter and commence the final fight/boss, the Player needs to be scanned by a device which will match his DNA with a database Playtime Co. has. The Player gets scanned and the voice says: "Welcome, X", identifying us by name for the first time. The door opens, and the player enters the Prototype's Boss Room.