The idea being Slaanesh’s birth is what made the other Chaos Gods really sit up and take notice of how much free psychic power an evil galactic empire of murder monkeys can generate, so when Useful Idiot McGenocide was ready to start conquering they made it so that he could and cleaned up Slaanesh’s afterbirth as it were.

Assuming the Chaos Gods have that kind of control over the Warp of course (I honestly don’t know whether or not they can cause warp storms, there’s still a lot of 40k lore that I don’t know that well). It’s possible as well that the Emperor knew when the warp storms would clear up and chose that time to start forming the Imperium to get ahead of the Xenos.

That is typical of 40k lore though, everything is left vague and having multiple possible interpretations, and story threads are started then abandoned all over the place. It’s all just to facilitate sales of model kits in the end.

Slaanesh was born after the Emperor conquered and unified Terra in M31. This cleared up the warp storms that had isolated most human worlds from each other during the Age of Strife and allowed the newly formed Imperium to begin to conquer the galaxy.