After all, the alchemy puppets and Alchemy Colossuses were sentient, and could be said to be not much different from intelligent creatures. They were fully capable of comprehending orders given to them without detailed control. The key was just who the commander was.
The controller of the Sky Castle was the highest controller of all the alchemy puppets and Alchemy Colossuses. Even if others managed to obtain the control hubs, the alchemy puppets and Alchemy Colossuses would still perceive the controller of the Sky Castle as the supreme commander, just like how the king was the supreme ruler to soldiers even though they would obey the commands of their generals. Not every general would be successful in coercing the soldiers to rebel.