Naked or Rubbed, makes no difference with the 3-2-1 method. The first couple of times I tried it I didn't have a clue about rubs, but the family did have a sauce we liked, so they got a coating during the last hour. The only variable I've got with the method is I do that last hour (really more like 45 mins) on my gas grill at a relatively low temp (250). I'll fire up just one end burner, bring the grill to temp, and place the racks of ribs away from the heat. Everything gets a coating of sauce, 20 or so minutes later a flip and another coat of sauce. I'll wait another 20 minutes or until the sauce has gotten mostly dry, remove and start the feast!
My biggest reason for going to the grill for the last step is I have better access to brush the sause on the ribs. No reason it can't be done in the smoker, I just have a hard time getting between the relatively narrow spacing of the smoker shelfs.
The 3-2-1 method is kind of like the "Pirate Code" - they be more like guidelines than actual rules! Best of luck. Let us know how they turn out!