Kondo was able to control him because the Dominion Bullets the emperor gave him were devised to be higher level than Alternative. If Damrada had learned Alternative naturally instead of receiving it as a gift, his body never would've been taken over. It was a real obstacle, and Yuuki had to use Anti-Skill to the hilt to break down the barriers. In time, though, he found the Dominion Bullet lodged in his soul, and once he had Damrada's permission, he instantly focused his power on it.