agreed, but that rather depends on how it's explained, actually. we learn it as an intellectual exercise, but the transition to physical training tends to be stunted by the fact that the "external" manifestation of the action is identified and imitated by most in a way that changes the "internal" mechanics (i think god just killed a kitten). to put it in a less ambiguous way, a kiai is a complex action requiring coordinating muscle contraction and breathing to maximize striking power, and is characterized by it's basic form resulting in a yell. when most people kiai, they think about yelling and simply yell their lungs out, instead of relaxing and focusing on the body/breath coordination required.
even more concisely: the problem is not THAT they think, it's WHAT they think. the most common case being thinking about something similar to what you instruct, instead of what you instruct, and thus failing to follow the instructions correctly.
The kiai becomes natural. when i do my katas and kiai without having to think about it. But its not natural at first.
If the other guy had said that, I'd be thinking "check out the big brain on other guy!" He didn't. Check out the big brain on Fish of Doom! Nicely said, dude!
Little story here. Was watching a forms demo and the guy was kiaing on a movement here and there with his staff. The funny thing was his Kiai. He(demo guy) said that his Kiai was Butol. But when hearing it, it sounded like he was screaming "butthole!". So he made a ferocious trusting movement with his staff and yelled "butthole!", I nearly laughed out loud.