Selection list from Array Unity - Random - GameObjects array

 using System.Collections.Generic;
 using UnityEngine;
 
 public class CheckpointsManager : MonoBehaviour
 {
     private GameObject[] checkpoints;
 
     private List<int> numbersList1;
     private List<int> numbersList2;
 
     void Start()
     {
         // Create an array with all GOs with tag "Checkpoint"
         checkpoints = GameObject.FindGameObjectsWithTag("Checkpoint");
         SetValidCheckpoint();
     }
 
     private void SetValidCheckpoint()
     {
         // create Lists objects
         numbersList1 = new List<int>();
         numbersList2 = new List<int>(); //list with selected numbers
 
         // Add numbers to numbersList1 using GOs array.Length (checkpoints.Length)
         // checkpoints.Length is the number of total checkpoints
         for (int i = 0; i < checkpoints.Length; i++)
             numbersList1.Add(i);
 
         // *** print numbersList1 values, just for checking them out...
         // foreach (int num in numbersList1)
         // Debug.Log("numberslist1: " + num);
 
         // *for loop used to add numbers to numbersList2 and checkout values
         // numbersList2 keeps the valid checkpoints values
         // if the random value is repeated (if it's already contained in numbersList2)
         // it is not added, and the loop counter is not increased
 
         int n = 4; // number of valid (desired) checkpoints
         for (int i = 0; i < n;) // i++ is applied only if the number is not repeated
         {
             int randNum = Random.Range(0, numbersList1.Count);
 
             // just for checking in console
             Debug.Log("choosen number: " + randNum);
 
             if (!numbersList2.Contains(randNum)) // if the list2 doesn't contain the randNum
             {
                 numbersList2.Add(randNum); // needed because we need to check out if number is repeated
                 checkpoints[randNum].tag = "ValidCheckpoint"; // change GO tag
                 i++; // increase the for loop counter
             }
             else // if the number is repeated
                 Debug.Log("number " + randNum + "is already included in numbersList2");
 
             // just for checking out in console
             Debug.Log("n2 list count: " + numbersList2.Count);
 
             // just for checking out in console
             foreach (int num in numbersList2)
                 Debug.Log("+++ numbers in numberslist2: " + num);
 
         }
     }
 }

Code without comments and others

 using System.Collections.Generic;
 using UnityEngine;
 
 public class CheckpointsManager : MonoBehaviour
 {
     private GameObject[] checkpoints;
 
     private List<int> numbersList1;
     private List<int> numbersList2;
 
     void Start()
     {
         checkpoints = GameObject.FindGameObjectsWithTag("Checkpoint");
         SetValidCheckpoint();
     }
 
     private void SetValidCheckpoint()
     {
         numbersList1 = new List<int>();
         numbersList2 = new List<int>(); 
 
         for (int i = 0; i < checkpoints.Length; i++)
             numbersList1.Add(i);
 
         int n = 4; 
         for (int i = 0; i < n;) 
         {
             int randNum = Random.Range(0, numbersList1.Count);
 
             if (!numbersList2.Contains(randNum)) 
             {
                 numbersList2.Add(randNum); 
                 checkpoints[randNum].tag = "ValidCheckpoint"; 
                 i++; 
             }
         }
     }
 }

Now you have 4 not repeated random numbers that can be used as index for a list or array of valid checkpoints, and instantiating as well. You can copy/paste in VS for better visualization.