I don't know, he's called The Six Realms Sage which signifies the six ripple patters of the Rinnegan, as well as the six abilities that each correspond to the individual realms.
The only way I'd come to the conclusion that he didn't uncover the Rinnegan until much later, is if he was just considered The Original Sage prior to the Six Realms Sage. But, we don't have that kind of proof yet.
I agree that we lack the info but we must consider a few things:
. RS wasn't worshiped like a god before he faced the Juubi in battle, the name Sage of the six paths might have emerged as his fame grew after he was victorious over the Juubi, which would them give the " He got the eyes after he became Its Jink " theory some credit.
. We have seen Bijuu being defeated by exceptional yet not haxxed people, RS passed down the means to take out in the form of Bijuu sealing techs which were the means he used to finish the Juubi for good.