If the sage was the first to notice chakra he would have a disadvantage IMO because he didnt know anything previosly about it unlike years later when people had time to practice jutsu and perfect their chakra. Therefore that inclines me to believe that the sage had divine intervention, I have a theory that when the sage discovered chakra he also discovered something divine and maybe thats how he got the rinnegan. When you say migh guy and rock lee could have easily gotten that kind of body you are assuming that they are on par with raikage's stregnth, we know that might guy and lee are extremely strong, but why isnt guy a kage if he is so powerful. Raikage doesnt need the gates to draw his power, it is always a part of him he can use at will as well as his speed. guy is the same level of stregnth as kisame when hes not unlocking the gates. Thats why I beleive that the 3rd raikage is able to have a resilient body, because he made it so through hard work from the start but ill say this it is possible he has links to the physical aspect of the sage i wont deny that, but that is far from a magical understanding of his powers.