I don't think BM and KM can be compared to EMS and Rinnegan like you did. Not trying to knock your hypothesis, but the sharingan and all it's variations is a BLOODLINE trait. As in it's apart of the Uchiha clan. Naruto gets his KM and BM from having Kurama inside of him. It has nothing to do with the Uzumaki clan or any form of heritage. I think that little fact kind of opens up a lot of holes in this theory.
It seemed like you were trying to imply that Naruto could also get the Rinnegan because of his progressions in with BM and KM. Well, that just simply can't be true, for the reasons I explained earlier. I really do like the idea of the MS and EMS being progressions to the Rinnegan, but that's like saying only Uchiha memebers can obtain the Rinnegan. The So6p split his powers in two, Uchiha getting the eyes, and Senju getting the body. It seems kind of unfair if the Uchiha can progress to So6p status without the help of Senju DNA yet the Senju can't do the same on their own.
I guess I'm kind of asking you, if your theory is true then what is the progession that the Senju take to reach the Rinnegan? Or do you feel that they simply don't get it to have that ability. I don't think your explanation of BM and KM really makes sense at all. Also, maybe in order to open the Rinnegan, you need a certain AMOUNT of Senju and Uchiha DNA. If Harishima was the only one with enough power to help activate the Rinnegan, maybe Madara had no choice but to go after him instead of a lesser Senju. Just a thought. Plus, if he didn't need Senju DNA, wouldn't it have been smarter to take on Harishima AFTER he unlocked the Rinnegan?