How can i get a specific GameObjects to array without using FindGameObjectsWithTag?

In the first script i clone some GameObjects:

using System;
using UnityEngine;
using Random = UnityEngine.Random;
using System.Collections;
using System.Collections.Generic;
using System.Linq;

public class CloneObjects : MonoBehaviour
{
    public GameObject ObjectToCreate;
    public int objectsHeight = 3;
    [HideInInspector]
    public GameObject[] objects;

    // for tracking properties change
    private Vector3 _extents;
    private int _objectCount;
    private float _objectSize;
    private List<GameObject> cloneList = new List<GameObject>();

    /// <summary>
    ///     How far to place spheres randomly.
    /// </summary>
    public Vector3 Extents;

    /// <summary>
    ///     How many spheres wanted.
    /// </summary>
    public int ObjectCount;
    public float ObjectSize;

    public static float LargestSize = 0;

    // Use this for initialization
    void Start()
    {
        Clone();
        //objects = GameObject.FindGameObjectsWithTag("ClonedObject");
        objects = cloneList.ToArray();
        foreach (var element in objects)
        {
            float Size = element.transform.localScale.x;
            if (Size > LargestSize)
                LargestSize = Size;
        }
    }

    private void OnValidate()
    {
        // prevent wrong values to be entered
        Extents = new Vector3(Mathf.Max(0.0f, Extents.x), Mathf.Max(0.0f, Extents.y), Mathf.Max(0.0f, Extents.z));
        ObjectCount = Mathf.Max(0, ObjectCount);
        ObjectSize = Mathf.Max(0.0f, ObjectSize);
    }

    private void Reset()
    {
        Extents = new Vector3(250.0f, 20.0f, 250.0f);
        ObjectCount = 100;
        ObjectSize = 20.0f;
    }

    // Update is called once per frame
    void Update()
    {

    }

    private void Clone()
    {
        if (Extents == _extents && ObjectCount == _objectCount && Mathf.Approximately(ObjectSize, _objectSize))
            return;

        // cleanup
        //var ObjectsToDestroy = GameObject.FindGameObjectsWithTag("ClonedObject");
        var ObjectsToDestroy = objects;
        foreach (var t in ObjectsToDestroy)
        {
            if (Application.isEditor)
            {
                DestroyImmediate(t);
            }
            else
            {
                Destroy(t);
            }
        }

        var withTag = GameObject.FindWithTag("Terrain");
        if (withTag == null)
            throw new InvalidOperationException("Terrain not found");

        for (var i = 0; i < ObjectCount; i++)
        {
            var o = Instantiate(ObjectToCreate);
            cloneList.Add(o);
            o.transform.SetParent(base.gameObject.transform);
            o.transform.localScale = new Vector3(ObjectSize, ObjectSize, ObjectSize);

            // get random position
            var x = Random.Range(-Extents.x, Extents.x);
            var y = Extents.y; // sphere altitude relative to terrain below
            var z = Random.Range(-Extents.z, Extents.z);

            // now send a ray down terrain to adjust Y according terrain below
            var height = 10000.0f; // should be higher than highest terrain altitude
            var origin = new Vector3(x, height, z);
            var ray = new Ray(origin, Vector3.down);
            RaycastHit hit;
            var maxDistance = 20000.0f;
            var nameToLayer = LayerMask.GetMask("Terrain");
            var layerMask = 1 << nameToLayer;
            if (Physics.Raycast(ray, out hit, maxDistance, layerMask))
            {
                var distance = hit.distance;
                y = height - distance + y; // adjust
            }
            else
            {
                Debug.LogWarning("Terrain not hit, using default height !");
            }

            // place !
            o.transform.position = new Vector3(x, y + objectsHeight, z);
        }
        _extents = Extents;
        _objectCount = ObjectCount;
        _objectSize = ObjectSize;
    }
}

Before in the first time i used to give the children objects i clone a Tag name. So i could do:

var ObjectsToDestroy = GameObject.FindGameObjectsWithTag("ClonedObject");

But now i'm not using this line. So all the cloned objects are untagged. So now i'm not using this line.

But now i want to get all the cloned objects from another script:

void Start()
    {
        anims = GetComponent<Animations>();
        waypoints = GameObject.FindGameObjectsWithTag("ClonedObject");
        originalPosition = transform.position;
    }

But since the cloned onjects are without any tag waypoints will be empty. waypoints is array of GameObject: GameObject[] waypoints.

Should i give tag name to every cloned object ? Or is there any other way to get all the cloned objects into array/List ?