He wasn't thought of as a genius, he grasps concepts slowly until he gets hands-on practice, and he doesn't exactly come off as a genius through his demeanor. None of these things change the fact that he is, and always has been, a genius.
He learned Kagebunshin before he could even use his chakra to run up trees or walk on water. He learned mastered the Rasengan in a week. It should be no surprise that, years after these feats, he could master Sage Mode quickly. After all, Sage Mode is all about familiarity when sensing/controlling natural energy. Once these acts become more routine for Naruto, he can become faster at them.
As for mastering the use of Bijuu chakra, the chakra literally feels like an extension of his body, and he can also draw from his years of experience controlling human, Bijuu, and Sage chakra. Naruto is just extremely familiar with balancing different types of chakra.
