So is Kishi's explanation for the senjutsu beating the ten tails' natural energy just going to be Naruto's "I dunno"? That's some bullshit right there.
I have suspected that maybe nature chakra acts like the white blood cells of the planet itself. When they encounter a foreign antibody that uses the polar opposite design they attack which results in the white blood cells pretty much damaging the foreign antibody. The reason the juubi is foreign is due to the fact that as far as what has become clear, it is not of their world and thus uses nature energy of its world. As a result its not recognized as native and therefore the nature chakra automatically increases its damage. On the other hand when senjutsu is used on anything that is of the same element it automatically acts like any other element would except when it enters the chakra stream of another entity. When it does so it automatically tries to reconfigure that person genetically to be handle nature chakra. If that person doesn't genetically adapt their turned to stone. Weird theory eh?