There are hundreds, maybe thousands versions of the origin of the Emperor: Whenever Adeptus Ministorum encounters a religion, it finds a way to put the Emperor somewhere there - if not as a main god in the pantheon, then as a deified hero (think Heracles or Gilgamesh). So most probably, the Eccelsiarchy put him into the important story from Abrahamic religions as a one of the first man.
The true origin is different: Thousands of neolithic shamans sacrificed themselves at the same time to create being with soul made of all those dead psykers, someone able to protect humanity from the encroaching Warp.
So what you are reading is either a Ecclesiarchy's half-forgotten propaganda... or a flat-out heresy.
Out of story answer:
While it is possible that the Black Library would try to retcon the origin, I doubt that this would happen any time soon. The official answer about information in BL books is that "everything is canon but not everything is true".