When did he did this combination attack with Yamato?If I'm not mistaken, Naruto did his Futon: Rasengan with a single hand when he used the combination attack with Yamato.
It's not a matter of mastery, it's a matter of preference. Naruto does it because that's how he learned it. Most likely it's just comfortable and out of habit that he does it that way.
It's not like it's ever cost him anything