We always knew that the Rinnegan comes from from Combining/mixing the Uchiha Mangekyou Sharingan (ultimate yin expression) with the Physical Energy of Senju/Younger son typified by Hashirama (Ultimate Yang expression), but this while TRUE, may not necessarily be all there is to the Rinnegan.
I suspect that the SO6P May have had a more complete pair of Rinnegans Which Sported Superimposed Tomoes, just like the Juubi has.
The Juubi from whom the SO6P derived his power, had both a Rinnegan and a 9 Tomoe Mangekyou superimposed, Yet The Sage seemingly, along with his descendants either had Sharingans or Rinnegans, but not both.
Madara's acquisition of the Sage's power may be incomplete. I note that Madara was able to perform Sharingan techniques while Manifesting a Rinnegan, but he never Manifested Rinnegan Techniques while manifesting his Sharingan. An example was, he summoned his Susanoo while using his Rinnegan. This could be because he lacked a more complete rinnegan
Madara with Rinnegan and Susanoo
We are keenly aware that neither the descendants of the Younger Son, the Senjus, nor the Younger Son himself possessed Rinnegans, but the Younger Son did have a glowing Aura around him, which the Senjus (the greatest of who was Hashirama) didn't have. Also, note that the Younger Son Had this Aura, but the Sage himself did not, from the images we have seen of him thus far. The glowing Aura is a visual manifestation of overflowing life energy, produced in excess and leaking out. In theory the SO6P himself lacked a glowing Aura because his excess life energy was being used to support a Tomoe superimposed Rinnegan.
So, the only example of a Mangekyou converting into Rinnegan we've seen thus far in Madara, converted ONLY, into a non-tomoe superimposed Rinnegan, and not into a combination Rinnegan and Sharingan, like the Juubi has. That Could be because The Senju Life energy from Hashirama (who had no visible Aura unlike his Ancestor, the Sage's Younger Son) could only advance the Mangekyou into a Tomoe-less Rinnegan. The question then is, What would happen if The Senju in question (supplying the Life energy to a Mangekyou) had had a Visible Aura?
I have searched for a Good (and Canon) closeup image of the SO6P's eyes, but I haven't found one, I don't think Kishi has given us one yet, BUT we do have this:-
Image behind SO6P
Looking at the image behind the SO6P (top left), it is enlarged in the center panel, we've always assumed that the eye in the image was the Juubi's eye. But it seems to me that this could be a depiction of the SO6P's own eye. This is highly suggested by the presence of the same flames the sage had in his hands in the top left image, and the fact that this image shows a Rinnegan with only 6 superimposed Tommoes, where the Juubi has 9 Tomoes.
If this is really a depiction of the SO6P's eye, then You will note that The SO6P may have had a Rinnegan With at least 6 Superimposed Tomoes, just like the Juubi has, excepting the Juubi has 9 tomoes.
The above observations have led me to formulate a theory That the Original SO6P was a lot more Juubi-like than Madara as a Sage. The Difference is probably because Madara stole Hashirama's power (life energy), but Hashirama Senju, as phenomenally powerful life energy as he had, was still diluted down when compared with The SO6P and The Younger Son. It is also possible that the same is true of Uchiha Madara, that his Mangekyo is diluted downward compared to the Elder Son's eyes.
It is again noteworthy that Sasuke has been pegged to have eyes that potentially will be able to surpass Madara's eyes, while Naruto also Has been Pegged to Surpass Hashirama. Naruto already glows with life energy like the Younger Son, When he is Using Kurama's power, such that Captain Yamato made mention of Naruto+Kyuubi's life energy activating his Mokuton.
My guess then is that Kishimoto is headed toward a Joint ultimate SO6P in Naruto and Sasuke together. (I really don't care too much for this idea, but I doubt that Sasuke will poke his own eyes out and give them to Naruto, nor is it likely for Naruto to take Madara's Sharingans although at this point it is not too much to conceive of Obito offering them to Naruto). It seems to me to be where things are headed, unless something like the DNA sword mutates Naruto into the Sage.
Bottomline Theory: (1) The real SO6P had Sharingans Imposed over Rinnegan, fundamentally because of greater life force than Senju Hashirama could provide to Madara. (2) Naruto or Naruto and Sasuke (together) potentially can equal or rival the Original Sage, and Manifest Juubi-like eyes.