You share some incredible insights to the development of your project! The idea of storing the story flags discovered sounds like a genius idea to determine which articles should spawn in. The entire system seems very organized!
I also ran into the problem of storing data between scenes in our game and also used Scriptable Objects in a very weird way. Ture heroes.
Also, a neat thing you can do with Scriptable Objects is use them as the middle object with Unity Events! When something happens like the player drags in an image in the newspaper, it will invoke a Unity Event inside the scriptable Object. And then another object in the scene can listen to when that event in the scriptable object is called and run a method if it is! It's a great way to remove dependencies in your scene objects.