Dunno if what i'm about to say fits in the lore, but there is a theory that can explain the "bargain" happened in Molech: Dark Age of Technology - Age of strife.
Both sides made a risky bet: The Emperor got access to misteries of technology, thought he can overdue the drawbacks with things like the access to the webway (maybe even the knowledge needed to make Primarchs/Space Marines), the Chaos Gods thought that whatever things men will achieve, the corruption of the machines (and almost anything related to that knowledge, Primarchs included) Â will be a huge success, leading to the Age of Strife just to begin...
On certain degrees, we can say both sides get something and lose something else.
Emperor got the Golden Throne, he was just inches away to realize an imperial webway, he has Custodes and Space Marines, and still today the most fearsome weapons and tech the imperium can field are related to that leap in technology, considering the Mechanicum is still in search of STC and anything related to that time frame is vital for them.
Chaos Gods gain the Age of Strife, disrupting the Imperium in a shocking and irreversible way, STC can still be corrupted or already are, proven to be exceptional weapons in their hands, and they deprive the imperium of men of anything concerning A.I. , not forgetting the traitor Primarchs later on...
It was a bargain both won and lost...like every bargain between sides that don't trust each other 100%.