So wouldn’t it be easier if Naruto used nature energy to turn the bad guys into toads in Boruto when they absorb his chakra
In Boruto, their absorption isn’t straight up energy like Nagato. The Ototsuki absorbed jutsu and then used their abilities to send back a magnified version out of their own chakra. Also, the maximum capacity of chakra in an Ototsuki is either equal to or higher than Naruto’s as their race grows by eating ten-tailed beasts. If I recall, the only other instance of jutsu absorption was the robot girl. I can’t tell you how robot ninja powers work so I can’t say whether this would work or not.
He does it in the Pain fight, so yes. The problem with Boruto is that he has to somehow be necessary enough to the plot to be the main character. This means Naruto has to be nerfed or indisposed. Very unfortunate. (Also why I don't like Boruto.)