Regardless of any middleware, the same rules apply for any loading/saving: it is an engineering decision driven by the economics of effort vs tradeoffs vs features desired.
Load/Save steps:
Don’t use the binary formatter/serializer: it is insecure, it cannot be made secure, and it makes debugging very difficult, plus it actually will NOT prevent people from modifying your save data on their computers.
When loading, you can never re-create a MonoBehaviour or ScriptableObject instance directly from JSON. The reason is they are hybrid C# and native engine objects, and when the JSON package calls new to make one, it cannot make the native engine portion of the object.
Instead you must first create the MonoBehaviour using AddComponent() on a GameObject instance, or use ScriptableObject.CreateInstance() to make your SO, then use the appropriate JSON “populate object” call to fill in its public fields.