Nothing is being contradicted, nature chakra is seperate from his own, that's why he can have clones gather it for him.
The clones are also exact copies, any jutsu naruto can do they can do as well obviously, so them creating more clones isn't a contradiction and it can be assumed that it will split chakra only between themselves since it's being recast as a "new" user.

All clones naruto makes in sage mode will also be in sage mode, meaning if one of the clones he left behind would to split itself, it would effectively half the nature chakra it had gathered, giving naruto only 1 shot of a rasenshuriken if dispersed instead of 2.
Also the clones were completely immobile and could only focus the nature chakra, even when reversed summoned they didn't move at all; naruto clearly stated that the 2 clones focussing nature was his max, 1 more and they'd lose focus.
That's also why he only had 3 clones to fight pain, 4 fighting clones would also disrupt the focus.