My opinion is that the 9 tomoe is eye native to the juubi, not the sage. But its too coincidental that the 9 tomoe so closely resembles the Rinnegan and its watered down version, the sharingan. So basically there has to be more too it, but I still feel that the 9 tomoe is native the the Juubi and that perhaps his chakra being in the sage is what spawned the later sharingan mutation.