Don't you get it? Remember how the Kyuubi's eyes looked like when it was being controlled by Madara. It had sharingan eyes. That's why the Juubi has Rikudou Sennin's eyes/eye. It's being controlled by him. In order for the Rinnegan or the Sharingan to awake inside your body you have to be born with it.
The new chapter coupled with the last few ones tell a different tale.
Doujutsu has been connected with hatred and evil, while sage techs and physical strenght/powerful body to good. ( see the two sons )
Since the younger son inherited the sage's body its logical that RS had an extremely powerful body himself. Doujutsu has been defeated by force before so a RGless RS defeating the Juubi is not far feched.
After he became its jink RS became the ninja equivalent of a god, since there is no proof that he had the RG before he became a jink it could very well be that he acquired it afterwards.
Now this makes sense to me for a few reasons:
. We havent seen RS with SG aspects, and since the SG has been connected to hatred it could be that RS supressed the darker half of the Juubi much like Minato did with the Kyubi.
. Since the Juubi is something of a deity itself, due to its massive power affecting RS's gene pool could have been a byproduct. Therefore giving bith to doujutsu which manifested itself in the Uchiha clan as the dark haf, while his physical power manifested itself in the Senju.
. As for Madara controlling the Kyubi, now there is a connection. If the Juubi is the genesis of all Doujutsu, the fox being one of its pieces would react to the SG.
Obviously this line of thought has holes in it such as the BG ( it has to be a mutation at this point, its just too weak ), and why the RG didn't manifest at a mass scale like the SG.