I dont think Rikudou Sennin had to go through genetics at all. I think the whole "RS was Uchiha and Senju" is simply that he had both powers, not that he was literally carrying the DNA of these bloodlines who didnt even existed. I think RS simply had a massively strong body or was a super sealer like the Uzumakis were, then when he got the Juubi which according to Tobi is what made him a god, he got the Juubi's eye and also his body got strenghtened further like that of a Senju just as how Naruto's body change when he is using Kyuubi's chakra.
Remember the Bijuus have active and latent traits that pass to their jinchuurikis, for example Naruto having whiskers and Kushina having hair that move like tails is a passive trait of the Kyuubi, Naruto having a shroud and Kyuubi powers is an active trait, something he gets when going jinchuuriki form.
I think the same applied ot the RS, but as the Juubi is on a completely different level his passive and active traits are so too. RS didnt had the Rinnegan and it is possible he didnt even had the super strong Senju body, but was simply a massive sealer (maybe RS was an Uzumaki), then when RS got the Juubi as a passive trait instead of getting whiskers he got the Juubi's eye minus the sharingan tomoes, aka the Rinnegan was when Rikudou wasnt using the Juubi's chakra also his body got super strenght merely for having the Juubi, then when using the Juubi chakra he would have the Rinnegan with tomoes and bodily transformations like that of Naruto's. After having sons then he passed to them with genes his super strong body to the younger son and a diluted version of the Rinnegan to the elder son.
Rikudou didnt went through genetics, he was the real man, he outright went for it without the need of magic genes. Basically the Senju and Uchiha are simply a genetic version of what Rikudou achieved himself.