Khan didn't have [The Pure Trees]'s azure symbols to bolster the trio's perception. He didn't even know how they worked. Things might have been different if he had studied them with his current senses, but Nitis was outside his reach.
Khan wasn't even sure how to teach that field. His perception had always been naturally good, and the transformation had pushed it to a superior level. He was a natural, and Nitis' perfect environment and his mindset had only highlighted that talent.
The Global Army had techniques and training regimens that could improve the soldiers' perception, but everything felt artificial and unnatural when Khan looked at them. So, he decided to develop something better suited to his knowledge and style.
Initially, Khan had considered manipulating the trio's energy through his influence. He had already succeeded with Roger, and that process would also improve his journey toward the mysterious evolution past mana.