You're conflating authority, the authorization to do something, with autonomy - the ability to use that authority at your own personal discretion. The law grants a regulatory agency the authority to do something that they would not otherwise be able to do, like nationally ban widgets. But the law does not also inherently grant them to the autonomy to do so entirely at their own discretion. For agencies under the Executive branch, the President is free to direct them to utilize their authority at his discretion.