Wft are you talking about. Too many mistakes.Naruto already showed SM and KM can be combined in the Pain ark and how do they represent 2 different things if Sage Mode is adding natural chakra with your own and Naruto's Kyuubi Mode chakra gives off living energy (stated by Yamato when KM chakra reacted with wood element). Sounds like they go perfectly together. And you facts about element chakra are incorrect. Every ninja is born with at least 2 different affinities that they either got from one/both of their parents or randomly got, it's rare for a ninja to have 3 affinities like the Mizukage or that old kage(dust element). The Sharingan allows the user to copy any jutsus that use any of the 5 basic elements (earth, water,fire,lightning, wind) from any opponent but they can't copy jutsus that use elements that are combine from 2/3 other elements (wood, dust, boil), bloodline abilities or certain jutsus. The Rasen Shuriken is an example of a certain jutsu from a above, since the Rasen Shuriken is made by adding wind chakra to chakra manipulation it proved to much for kakashi to follow with his Sharingan. There's a differences between using a jutsu that uses wind element and a jutsu that you have to combine with wind chakra, you need the wind chakra to combine with chakra.
Youve got the whole, chakra affiliation techs wrong. I'll simply say to you that go back and watch the fight between kakashi vs kakuza and note what kakashi says about kakuzu being able to use all 5 s-rank chakra affiliation techs.
Also what you fail to get is that, no body has a 100% chakra affiliation. Naruto for example, most dominated chakra affiliation is wind. Thats what, but that isnt 100%. He might have 70% wind chakra, 20% earth and 10% water. Whilst he might be able to use earth and water techns, he cannot use s-rank techs from these elements, whilst he can use s-rank techs from wind.
On the uchiha issue. All uchiha's would have 2 element chakra afflition. Fire which is from their bloodline and other which is their own. In sasuke's case, its lightning, itachi's case water and if im right, in madara's case wind.
As for the sm and km mode combined, sure this happened for a brief moment in time, but it would never happen again.