Now you are just wrong, both physical energy and spiritual energy are required to make chakra. If you lack one or the other, you wont have much chakra. you dont have Spiritual Chakra and Physical Chakra, rather, they are different kind of energies that need to be combined in order to make Chakra. You need to keep them in balance; that means that if you are lacking one, the other by itself will not be enough to produce a large amount of chakra, nor a little amount of powerful chakra. Sage techniques just add Nature's energy to the molding process.
You must be registered for see links
And i know that Naruto has a very large amount of chakra of his own, but we will never now just how much, because he has the Kyuubi. Besides, what makes you think that Sasuke (just an example) could not supress the Kyuubi's chakra too? I mean, he succesfully supressed Orochimaru, and according to you, he was related to the Senju.