.. Rasenshuriken is not a physical attack it is a chakra based attack...
A chakra based attack that does physical damage. If the system was completely unhealable then when Naruto damaged his the first time it would have been permanent. But it wasn't; only repeated minor damage or massive damage leads to permanent disrepair.
I don't believe it's ever been stated that your chakra just clouds around your body, for instance, so it would not be a good thing to assume just because of how something was animated.
There's just so many times it could have come up if it was physical and did not. When Lee had his surgery after the Konoha Crush it was problematic because fragments of bone were lodged in his spine. Extracting them from his spine was the problem, not the chakra system that is supposed to be tied to every cell of your body.
Again how did Hagoromo giving people chakra work if it requires a physical structure for transport? Did every living creature just instantly grow one? That's a little much even for Naruto.
To my knowledge, when the sharingan vision was being shown even in the manga chakra was shown around the body at least like an aura.
Lee is not chakra obligate for his style of fighting, or at least he wasn't when that arc was up and active. Him not being able to manipulate chakra paled in comparison to outright death.
I wasn't going to jump in on this discussion because it doesn't really interest me, but you've butchered some concepts in your post so I felt compelled to do so.
1) ATP is the molecular unit of intracellular energy transfer. It's not directly converted to heat. Heat is the transfer of energy from a hotter object to a colder object.
2) You said, "energy is neither destroyed nor created". That's incorrect. The First Law of Thermodynamics dictates that energy is neither created nor destroyed, but simply changes form. The Law of Conservation of Energy dictates that the total energy of an isolated system remains constant.
3) Absorbing heat is not similar to "absorbing" ATP (cells don't absorb ATP, that would be a gross oversimplification). When heat is absorbed by an object, the velocity of that object's molecules increases, thus increasing the temperature--temperature is a measure of the average kinetic energy of the molecules in an object.
(1) Fair enough.
(2) Why does the specific order of the words matter in this context?
(3) A gross oversimplification was the intent here. Chaka is a combination of spiritual and physical energies; what kind of energy they fit into when applying concepts from Physics, I feel, is overcomplicating things when the point is that energy is converted into different forms that may be more viable for absorption by external techniques.