We know that from the Juubi's point of view, it saw the Bijuus' chakras inside Naruto:
But another peculiarity was that the Juubi saw Rikudou's image in Naruto:
Which made the Juubi visibly distraught:
That same imagery of Rikudou appearing in Naruto mirrors that of when Nagato's Chakra flowed into Naruto when he was stabbed by Pein's chakra rod:
(Nagato's flowing chakra above and Rikudou's chakra flowing below)
It is because what the Juubi saw was Rikudou's Chakra essence inside Naruto.
I seriously doubt that the Juubi just remembered Rikudou in Naruto, you can clearly see that the Juubi sensed the Bijuus' chakras inside Naruto (Hachibi was not present) so it only stands to reason that Juubi also felt Rikudou's chakra inside Naruto which is the following panel.
Like I've hypothesized more than 2 months ago:
The Rikudou Sennin's Chakra essence is sealed inside the Bijuus (much like Minato and Kushina's chakra were inside Naruto)
That aside from Naruto receiving the Chakra of the Bijuus:
Naruto also acquired Rikudou Sennin's Chakra sealed inside the Bijuus (The same Uzumaki Fuuinjutsu Kushina and Minato used to seal their chakra essences inside Naruto)
Even Tobi/Obito realized that there is something different in Naruto and not because of the powerup the Bijuus gave him:
I think it is only a matter of time before Rikudou Sennin completely manifests inside Naruto, possibly when he receives the Yin Half of Kurama's Chakra Rikudou will finally emerge. And Rikudou Sennin himself will tell his own flashback concerning him and the Juubi.