Reference to scene objects from scriptable objects

This may not be the best practice, but if it were up to me I'd just attach a script to the desired objects that tells them to add themselves to a list within the ScriptableObject (in Start and/or OnEnable). You'll probably also want to make the same objects remove themselves from the list in OnDisable.

Here's a simple example of one such script:

 using UnityEngine;
 
 public class AddToScriptableObjectList : MonoBehaviour
 {
     // Reference to the ScriptableObject
     [SerializeField] SceneReferenceSO sceneReferenceSO;
 
     void Start() => AddSelfToList();
     void OnEnable() => AddSelfToList();
     void AddSelfToList() => sceneReferenceSO.objectList.Add(this.gameObject);
     void OnDisable() => sceneReferenceSO.objectList.Remove(this.gameObject);
 }

You could then give the ScriptableObject some basic logic that empties out the list each time a new scene is loaded so that you don't end up with any broken/invalid references belonging to previous scenes, like so:

 using System.Collections.Generic;
 using UnityEngine;
 using UnityEngine.SceneManagement;
 
 [CreateAssetMenu(menuName="Scene Object References")]
 public class SceneReferenceSO : ScriptableObject
 {
     public List<GameObject> objectList;
     
     void OnEnable() => SceneManager.sceneLoaded += OnSceneLoaded;
     void OnDisable() => SceneManager.sceneLoaded -= OnSceneLoaded;
     void OnSceneLoaded(Scene scene, LoadSceneMode mode) => objectList.Clear();
 }