Just manage one asset file to initialize any Prefab by the runtime, so Prefab will initialize one by one whatever what scene you are running.
Just copy the "RuntimeInitializer.cs" to your project Assets folder.
- In the Unity Editor, go to menu bar Assets > Create > RuntimeInitializerSetting.
- Edit the "RuntimeInitializerSetting" asset file, and choose any prefab you want to initialize by the load type.
More details about the load type, please check: https://docs.unity3d.com/ScriptReference/RuntimeInitializeLoadType.html