I agree, Prime Naruto and Sasuke are pointless, but for different reasons. We are never going to see them in their prime because they will never fight an opponent as powerful as kaguya or Madara.
You are right. I have read many summaries and a few several short videos from the movie and Naruto never uses rikudou mode. 90% of the movies Naruto is fighting in base mode. So he didn't lose it, he just never used it.
Naruto used the all the tail beast power to help cancel IT after his battle with Sasuke. He used up all of the chakra he had in battle. They proves he permanently gained their powers.
People need to understand Sage might have used chakra to transfer those powers to Naruto and Sasuke, but they permanently gained those powers.