Most Liga teams have an excellent scouting system. Sevilla and Villarreal have even better ones imo. The difference between Atlético and most other spanish teams is that they have more money, larger fanbase, greater appeal for football players, stronger power to retain their players for longer, and an absolutely world class manager.
Even though Cholo says Koke and Godín are the only players he considers irreplaceable, it's him the one that the club can't afford to lose.