Imo, Marotta and Paratici are also getting a percentage from these transfers.
Marotta was the mastermind. He alone was getting 40% from every transfer. Once he left, he made sure that Paratici will replace him, and they shared the 40% commissions 20% each. Paratici made sure that Giuntoli will replace him (the guy between them was just a puppet). Now Giuntoli is getting 20%, while the remaining 20% are shared between Marotta and Paratici.
In other words, if we pay 50m for Koop, Atalanta will receive 30m euro (which is the real price), Giuntoli will get 10m, while Paratici and Marotta will get 5m each.