I think a few people are getting off topic and others are adding their own personal beliefs of the narutoverse.
Most of my speculations stem from manga facts and I also have created a thread comparing the abilities of Naruto's Senjutsu to his Kyuubi's powerups.
Here is a link..
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Starting from you're initial post, this is true. The Juubi's energy and the world they live in share the same chakra. The Juubi is indeed the fabled tree of life. Therefore the Juubi is the world/planet, Nature itself.
ALL other forms of chakra are manipulations of this original energy therefore that is the only thing that could stop it.
The entire flaw in your argument is that senjutsu disrupts chakra where it is as someone stated the art of collecting nature chakra. Falling under a genjutsu means someone is controlling you're chakra. Meaning even if you are a tailed beast who has more chakra than someone else, you can still fall under the spell.
The only way to release a genjutsu is for someone to force their chakra into you to disrupt your flow and regain control. Think of it as a reset button. An Individual does not have this ability with or without sage mode.
Moving to your next statement, it is true Itachi *said* only someone with MS could break it.
If you read deep enough into the manga or understand the small details that are taking place you would come to the conclusion that yes Sasuke had 3 tomoe but he also was in possession of the cursed seal mark at the time. Which is, senjutsu based..
Everyone knows Madara needed Hashirama's DNA to unlock Rinnegan. MEANING Uchiha + Senju = Sage6Path.
Sasuke Uchiha blood mixing with the senjutsu of the cursed seal gave Sasuke Rikudou powers. I also doubt itachi knew of the powers of Senju as most of them seemed to be extinct and the last known user was Mintao who died when itachi was still young.
Addressing other things.. Kabuto no did not achieve Rikudou Senjutsu, he peaked at the level of the Sannin, which is basically naruto's Sage Mode. Without Rikudou powers or a tailed beast, he would be unable to escape genjutsu. Especially one of that power.
Another point, someone said Sage Mode and RSM are not very much different.
I implore you to look at the difference in amount of time it took for nature to achieve both of these things. If RSM was not a sufficient powerup. He would have got smacked around by pre-juubi Madara.. again.
Naruto and Sasuked DIED! quite easily.. to a single eyed Madara. Once he achieved juubidara. It would not make any sense of RSM =SM in any semblance. They are worlds apart in size of jutsu and chakra manipulate.