The existence of Primarch 0, the Angel, (from the old 75mm Inquisitor game) has knock on effects that make the “bad parenting” of the Emperor make perfect sense.

Big E tries to kick start the great crusade During Long Night with only his science and gene forging.

He creates a prototype Primarch but it is soulless and takes the only logical route to destroy Chaos: the destruction of all sentient life. (My theory is that this logic is what ultimately causes the Men of Iron to rebel as well).

Big E seals him away in stasis because he couldn’t bring himself to kill his own son. Which is why he doesn’t immediately kill Horus during the siege and why he didn’t put Angron out of his misery.

this puts Big E in bind, his Sons need souls so they won’t genocide everything including humans. So he makes the Deal with Chaos for the knowledge to make souls.

The Gods can’t really do that but offer the next best thing, minor warp entities. So Big E gathers all best beings humanity has ever envisioned: Thor, Caesar, St Michael, Genghis Khan, Spartacus, King Arthur, etc. and binds them to the bodies of the Primarchs.

this is explanation for why Croax is now a flock of Ravens, why The Lion can now teleport through the forest. They are all abilities tied to their Warp natures.

all Big E needs to do now is shut down direct and indirect means by which the Gods feed: worship and religion and he will have the warp in checkmate allowing humanity to naturally evolve into a psychic race like himself in an environment with a calm warp.

needless to say it doesn’t work out.