is there difference between an instantiated prefab and one thats been manually dragged into the scene?

hi there, Im making a VR game and my player prefab is obviously a little more complex than normal with the different colliders and sprites that are on the actual player. If i Drag my player in, doesnt matter if it 20 feet above ground, underneath the ground, it always works properly. But when i instantiate the very same prefab somehow my inventory is either 10 feet above or below me. It seems almost like the different object collide separately and it offsets the position of the children of the prefab... Im honestly stumped... I am trying to create a random Player start position... a simple idea... but apparently not for me. seems to have to do with the prefabs relationship with the children object any help would be greatly appreciated.

 public GameObject player;
 public Vector3 startPos1;
 public Vector3 startPos2;
 public Vector3 startPos3;
 public Vector3 startPos4;

 private Vector3 SpawnPos;

 public int ranNum;
 // Start is called before the first frame update
 void Start()
 {
     startPos1 = GameObject.Find("PlayerStart1").transform.position;
     startPos2 = GameObject.Find("PlayerStart2").transform.position;
     startPos3 = GameObject.Find("PlayerStart3").transform.position;
     startPos4 = GameObject.Find("PlayerStart4").transform.position;
     PlayerDrop();
 }
 public void PickYourPlace()
 {
     ranNum = Random.Range(1, 5);
     if(ranNum ==1)
     {
         SpawnPos = startPos1;
     }
     if (ranNum == 2)
     {
         SpawnPos = startPos2;
     }
     if (ranNum == 3)
     {
         SpawnPos = startPos3;
     }
     if (ranNum == 4)
     {
         SpawnPos = startPos4;
     }
 }
 void PlayerDrop()
 {
     PickYourPlace();
     Instantiate(player, SpawnPos, Quaternion.identity);
 }

}

heres a picture showing in the very first frame the two prefabs are not identical, blue is the prefab i manual place and red is the instantiated one. hard to tell but you can see the orientation of certain objects or off