The documentation was indeed misleading, Baker.IsActiveAndEnabled checks if the GO is active and the component(behaviour) is active ánd enabled. In the case of a Behaviour, enabled means 'added to MonoBehaviourManager'. Because the MonoBehaviour of a prefab is not added to a manager, as it's monobehaviours are not supposed to run until the prefab is instantiated, it will return as disabled. Note that this is not related to enabling or disabling the MonoBehaviour in editor and also not unique for DOTS; all MonoBehaviours on prefabs will return disabled in every case. I changed the documentation.