My take on Amir's footwork are, his hands are always moving faster than his feet. Thus, he always gets out of position to defend himself. Happened in the Maidana fight, this fight, the Devon fight and the Algieri fight. He doesn't set his feet (as you said) and ends up throwing arm punches, which he can't bring back fast enough to guard his face. Even if Khan lands that right uppercut he's trying to throw, he still ends up getting KTFO b/c that'd end up being a temple shot.
My thing about that punch is Danny turns it horizontal as it goes over the shoulder, and doesn't bring the knuckles around to hit the neck--he keeps them horizontal until Khan damn near hits the ground. Never saw that before his fight with Guerrero, and krack found that lovely footage of SOG practicing that punch for the exact situation Danny was in. shyt is fiya.