Board Thread:Theories and Speculation/@comment-30355627-20161218164138/@comment-734582-20161219082950

Keaire wrote: Are you saying, because Sasuke's ocular powers were weakened, this proves that his left eye isn't a merger of chakra powers? You don't think it's strange that his Mangekyou specifically is weakened, but his Rinnegan power is intact? He can't even cast Susanoo while Madara didn't even need eyes for that. But an ultra-high level jutsu like Amenotejikara which he can only cast a few times, is still available.

So yea i think it clearly establishes his eye as having both dojutsu but also separate, since it's clear the tomoe are a manifestation of his Mangekyou.