Well I'll break it down the best way I can. Firstly, this movie should not be a representative of the real Naruto. Why? It's a pairing thing. Kishimoto did not want to make this wholeheartedly as a real movie, but merely Studi Perriot decided they wanted to make a movie on Naruto and Hinata's love. Taking that for understanding, we should already know to base our facts on this movie from the manga instead of the last "K-11" movie for Naruto. Which didn't really show any of the characters.
Firstly in the movie itself, Naruto displayed feats that wouldn't really consider it to be cannon in KCM/BM form. Such as: Flying, removing a chakra substance from Hinata's body, and one more (which I wil explain below). No idea how he could do any of these without some special type of chakra: Rikudou.
Anyway, the reasoning for the Last movie showcasing Kakashi as the Hokage is no big deal. Kishimoto had to have told SP he wanted to make Naruto the 7th Hokage, as he was too young. Nothing major.
Now Sasuke using the Rinnegan scene. That is the important part of this. The scene was literally for 35 seconds in total, and Sasuke in the scene had to use the Rinnegan to save the village by teleporting to Hiashi after destroying the meteor and exiting. In his 35 second show time I'm sure it wasn't hard to implement the Rinnegan itself, so there goes that scenario.
Now onto why Naruto most likely didn't use his Rikudou power up is for these two reasons:
1. They wanted to save it for the anime
2. They didn't want to nerf the form to equal a base RSM power which was standing against Kaguya.
I mean taking that into account Sasuke never fought anybody with his Rinnegan in the movie, so why would they need Naruto to use RSM against a weak version of JJ Madara?
The last scene of Naruto vs Toneri, he turned off his KCM form and a orange chakra started to form on his right hand which gave him a strange power to run straight through Tensagian-monster Toneri chakra blast attack. I cannot break down the scene with Naruto-logic. He literally just went straight through the attack without creating an attack, just an orange arm. He then re-created another arm on his left, and punched Toneri while shattering the moon surface.
Lastly: If it is not stated in the manga, it does not happen anywhere else.
What we know about Naruto/Kishimoto:
Naruto equals Sasuke (When does BM = Sharringan :l)
Kishimoto would never nerf the MC
That should be enough evidence to have a stable mind and destroy claims of him losing a power that was intended to st ay. He is Ashura's transmigrate after all.
