Vector3.MoveTowards and Quaternion.RotateTowards

I don't know exactly what you're doing, but suppose that you have an array of positions/rotations and want the object to move at constant speed and rotate smoothly from point to point. If that's true, I suggest you to use Quaternion.Slerp and Vector3.Lerp instead: since both are controlled by a float value between 0 and 1, they will always stay in sync. In order to keep a constant speed, calculate the movement duration and vary the control variable at suitable rate.
Supposing that you want to move from pointA to pointB and rotate from rotA to rotB at the same time, you could use something like this:

 var moveSpeed: float = 5;
 
 private var moving = false;
 
 function MoveFromTo(pointA: Vector3, pointB: Vector3, rotA: Quaternion, rotB: Quaternion){
   moving = true; // it's moving now
   var dist = Vector3.Distance(pointA, pointB); // find the distance to travel
   var duration = dist / moveSpeed; // calculate the movement duration
   var t: float = 0; // t is the control variable
   while (t < 1){
     t += Time.deltaTime / duration; // t varies at calculated rate
     transform.position = Vector3.Lerp(pointA, pointB, t); // move...
     transform.rotation = Quaternion.Slerp(rotA, rotB, t); // and rotate
     yield; // let Unity free till next frame
   }
   moving = false; // movement finished
 }

The boolean variable moving is true while the object moves: when it becomes false, you can pass to the next point. In the example below, pos and rot are the positions and rotations arrays, and setting moveBack to true makes the object move back to the first position:

 var pos: Vector3[]; // positions array
 var rot: Quaternion[]; // rotations array
 var moveBack = false; // true to make move back
 var curPos: int = 0;
 
 function Update(){
   // if must moveBack and isn't at the first position...
   if (moveBack && curPos > 0){
     if (moving) return; // do nothing while moving
     var nxtPos = curPos - 1; // find the next position
     MoveFromTo(pos[curPos], pos[nxtPos], rot[curPos], rot[nxtPos]);
     curPos--;
   }
 }