What I feel is that all these concepts have been created by keeping Chakra and the concept of Aura in mind.
What is an Aura?
According to the Wiki
Aura is a field of subtle, luminous radiation surrounding a person or
object (like the halo or aureola in religious art).
The size of an aura could be increased or decreased and it totally depends on the life force of the person.
What is chakra?
According to the wiki
Chakras are part of the subtle body, not the physical body, and as
such are the meeting points of the subtle (non-physical) energy
channels, called nadiis. Nadiis are channels in the subtle body
through which the life force (prana), or vital energy moves
Now if we consider that in Naruto when he increases his chakra, i.e. his life force increases which indirectly increases his aura dramatically (because of the immense chakra of kurama).
So what we can say is that, natural substances like rocks and stones that come into the influence of the aura, react to the life force of the user (here its Naruto).
As we've seen in many anime's (for example DBZ) [In DBZ we can call chakra as their energy]
Here you can see the aura of Goku clearly, its direction is pointing north (upwards).
So what we can conclude is that, the aura (at least in anime) moves upwards.
With this theory, I can say that whatever natural object that comes under the influence of an aura with strong life force, MOVES UPWARDS!
So the greater the aura and force, the more heavier objects would levitate.