Naruto has to learn now how and where he can let the nature energy into his Body and let it out. So it is some kind of experience or not? If he can learn how to use wind-element with his clones he should be able to do the same with nature energy.

And the power from Kyuubi is a "second source of chakra" which clones can use too. So why shouldn't the clones be able to use a "third source of chakra"?