"If you're going to use the Mangekyō Sharingan, then why not use Kamui directly? Wouldn't that be more efficient in battle? So... could it be that you're considering risk balancing?"
Kakashi Hatake's method of using the Flying Thunder God was certainly unexpected, and in some respects, it was even superior to the Fourth Hokage's first-stage Flying Thunder God. However, that didn't mean its combat efficiency was higher than using Kamui directly... assuming Kakashi could use Kamui with sufficient skill. Weighing the two options, since Kakashi had chosen the former, he naturally had his own reasons.
He had activated the Mangekyō Sharingan but hadn't used Kamui. What did that indicate? It meant Kakashi didn't need to take on such a great risk under these circumstances.
Sure enough, Kakashi explained, "If I only use this Sharingan to read spatial information—in other words, only to achieve the positioning effect of a Flying Thunder God marker—and then use the Flying Thunder God Technique to teleport, the risks of using the Mangekyō Sharingan are practically negligible. This way, I don't need to bear the dual mental and physical strain brought by Kamui. With Tenzo's Chakra helping me as well, I can use it as a regular technique."
The reality was that Kakashi was neither skilled at using Kamui nor the Flying Thunder God Technique. But by comparison, he was somewhat more proficient with the Flying Thunder God. In addition, he had better control over the risks of using the technique, so he preferred the Flying Thunder God. His whole strategy was to appear and disappear like a ghost.
"Can you teleport to a location without a marker? If so, you can catch your opponent off guard and even use Flying Thunder God kunai to mislead them... That's a little too invincible." Yuhara said this, but