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No, that special chakra as Rikudou confirmed is Rikudou's Chakra (as Hagoromo confirmed) and that Chakra
directly affects the optic nerve and sprouts the change in the eyes which forms the Rinnegan. Essentially, Dojutsu is the reflection of your own Chakra, so the Rinnegan contains Rikudou's Chakra.
You're not giving me any evidence as to why the Rinnegan doesn't contain Rikudou's Chakra. You're giving me pure speculation by claiming that it's just some strong chakra other than Rikudou's Chakra, but you don't even know what it is. Actually, Rikudou's Chakra is the strongest alongside the Uchiha's and Senju's Chakra, so if it's not Rikudou's Chakra, than what other Chakra is there that's even stronger than an Uchiha's and Senju's Chakra?