Then I remembered that the Age of Strife is when humanity's unstable psyker population exploded.
Which makes me think their alien allies were a tad bit freaked out when human beings began exploding into portals leading to hell and frying the brains of everyone around them.
They probably thought the species was utterly unstable and was going to wipe them out with their 'disease'.
Here's the thing though; a species that lacks Psykers is a rarity.
Humanity being incapable of birthing Psykers would make
them the odd and unnatural ones.
To the point where people believe that the Tau were artificially engineered or altered because they share that trait.
Why did humanity lack Psykers? Well....
Like, he comes off to me like for all his talents, power, and abilities he's still just another monkey hitting things with rocks, but Warhammer and his fans are all like "No, really he knows what he's doing becuase blahblahblahblah".
In my honest opinion, the Emperor is less than a character and more of a plot device meant to drive most of the story warhammer 40k. I've heard that authors that wrote scenes involving the emperor pretty varied their perception due to their own views; one has emps as a sorta ok guy, one writes him as the heartless pragmatic, and another makes him an incompetent douche. Honestly, GW should post a book series from the emperor's point just to get an actual solid identity on his character.
The Emperor is less of a character and more
several monkeys hitting things with rocks.
In 40K back during the Stone Age there were these people called "Shamans", which were literally just Psykers that were being honest about using space-magic instead of calling themselves psychics.
Some of them disliked how the world was and decided to change it, they did this through ritualistic mass murder-suicide;
Killing themselves and any of their number that disagreed with them in such a manner that all of their souls would be reincarnated into a single body.
While also stealing humanity's "potential"(read: psychic ability) for hundreds of generations.
The thing that resulted from this was the Emperor, who is actually a mental/spiritual gestalt of many different minds/souls rather than being an individual.
Yes, the Emperor is literally a bunch of cavemen, and cavewomen, duct-taped together on a spiritual level.
And the reason that he seems to have a different personality depending on who is interacting with him is because he uses his powers to determine the best persona to put forward to interact with people. This is much less effective on people who are closer to his level of power, like Malcador and the Primarchs.
Whether or not the Emperor was planning on something like the Age of Strife happening when humans could suddenly be psykers again is debatable.