This was never explained in the manga or anime. The only logical explanation I can give is that the "blades" would actually act as a physical manifestation of chakra, damaging Yamato and accidentally discharging his FR at Yamato causing an explosion radius that would also deal some damage Naruto.
However, the ball of chakra with chakra affinity combined (without the "blades") is not so much of a physical manifestation of chakra when compared to the FRS, meaning he was able to combine it with Yamato's technique with ease. Besides, it's less effective than the FRS so who cares? It's just one of those unexplained and plot-hole type deals.