Creating a scene: instantiating a prefab in a scene or use pre-instantiated prefabs?

I have created a complex scene for a simulation, containing cameras, rocks, waypoints, etc. Everything is created out of prefabs. I grabbed the whole tree of the scene, and created a prefab out of it.

At this stage, I have 2 ways of setting up a scene;

  1. I can leave the pre-instantiated prefabs as they are in the scene,

  2. Use a script to instantiate a prefab that contains many prefabs in a blank scene.

What are the pro and cons of both approaches as described above?

if you use option 1 you are going to avoid 1 more script, it better to load the full world in one time and then use and reuse objects of that scene, i recommend you to use option 1