I have a vague recollection of the Emperor, or someone else talking, about his origin and it being the shaman one. Can someone with access to the 5th ed BRB have a look at the timeline?
It is possible I'm having edition leakage here, 20+ years of background'll do that to you, but there are certainly plenty of hints and clues that the Emperor has been around since pre-history.
Re: Raven Guard. Corax goes to the Emperor's secret bunker to retrieve intel about the genetic manipulation that is the core of creating any of the superhumans but, as stated by the Emperor, it is the packed up remains of the Primarch lab.
The bunker is intended for future use by humanity as the Emperor knows his reign may one day fall (hence the Ozymandis line), and there is nothing sorcerous about the knowledge stated or implied.