yes charkra can be used to boost but it does not change the bones, muscle, and stuff, if not Gai and lee would not need to train their bodies now would they :). have you ever heard of the term a Glass container with Water this is what ninjas are, they can use water to temporary enhance the container but it does not change the fact that the container is Glass.
tsunade created a technique that compresses charkra in the fist and then explode on contact, this is what gives sakura her power but in fact is sakura does not exactly posses superhuman strength her punches do not posses Force is just a normal punch that has exploding charkra this is why her punches cause so much damage on structures liek buildings or the floor when compare to gai and his Gates, is because gai is carrying actual physical force and physical force is a compressed Punch in 1 point the energy does not spread like charkra, so in reality it might look like sakura is stronger but she is not.
Ninjas can still be hurt by Normal weapons like Shurikens and Kunais if they dont use Jutsu to block it, Lightning armor, Steel etc, charkra can boost defense but does not affect the internal Organs nor actual physical qualities of the ninja, and because of this charkra is an active source, the user must be aware of the attack to be able to block, for example lets take a character that has 100tons of force due to training with weights and stuff his body would be harder than steel and completely makes any shuriken and normal weapon useless he could be sleeping or even unaware of the strikes but his body would block it anyway because the body is passive defense it defends regardless or thinking or not, higher physique also brings the ability to withstand cold, fire and other envirements that a normal body cannot on the other hand charkra needs to be controlled. ninjas start extracting charkra by the age of 4-6, but these kids are normal they dont have superhuman strength, once they extract charkra they can jump several meters and use techniques to become faster and do various other stuff, think of it as Qi or Chi from Chinese wuxia/xinxia because that is exactly what charkra is based on in a sense, since the author did include the Charkra network which is exactly like meridians and charkra works almost identical to every xinxia novel that uses internal energy, this crap is very hard to explain if you rewatch naruto and analyze you can somehow come to a conclusion.
as for the bonus round it can either go to Deku or Gons team 50/50 since they both have versatility and instant kill moves, as for naruto team they would get stomped even harder, for example, Neji he would be completely useless here because his 64 palms and how it works, this techniques strikes the charkra points or meridians that carry the energy thus making the fighter useless, but this would be useless as Nen has a completely different system than charkra and even if it does have the same network gon is still superhuman even without Nen, when naruto fought neji and lost charkra he became fodder because as i said ninjas do not have a physical training system, 64 palms would be useless against anyone that does not have internal energy or a person who has both a strong body and internal energy like Gon.
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