In a nutshell, fraudsters buy keys from the official Factorio store with stolen credit cards. They then sell these keys on G2A and Factorio gets charged back (+fees) when the real owners of the credit cards report the transactions as fraudulent.
Ouch. The charge back fee is as much as the item.
In a world of 12% commissions (ie. Epic Games Store) the effort to sell directly wouldn't be worth it and G2A wouldn't exist.
Epic has also recently enabled keyless integration with some 3rd-party stores eg. Greenman Gaming.
That doesn't match what I've heard before, do you have a source? This site says that there is no fee to generate steam keys to sell directly, and in fact, you aren't even allowed to mark down the price of those keys. You are actually required to pocket the commission!
They still had to eat the $20 fee per fraudulent transaction and deal with the pissed off customers though.