Unitary Executive

With the Alito hearings, there has been a considerable amount of discussion about the "unitary executive theory" which is something that I have only recently become aware of. I mentioned that topic on January 6 in my "No Law" post. Much of the discussion in the Alito hearings concerning presidential powers focuses on this concept.
From what I understand, the unitary executive theory implies that the President is the head of all executive government agencies. None exist outside of presidential authority. Congress cannot establish any agency either fully or partially independent of the President. That actually seems to make some sense to me constitutionally. I'm not sure how the Congressional Budget Office fits into this framework. Wikipedia says that "is a federal agency within the legislative branch of the United States government.
I heard today that this theory was evoked one time by President Reagan, six times by Bush Sr., no times at all by President Clinton, and 110 times so far by Bush Jr. Clearly, Bush is using it to establish a new legal precedent, but the question is, what precedent are White House lawyers attempting to establish by using this theory?
It dawned on me this evening, and I was immediately rewarded with feedback from a discussion on Public Radio, that the unitary executive theory is used to define the scope of presidential power as total. That fits with Alito's 2000 comments about executive power. It also seems to fit with how the phrase is used in Bush's signing statements. By total, I mean the president is stating that the exception to law that he is establishing applies to all agencies of government under the authority of the office of the president. Nobody is excluded, not the military, not the State Department, not the CIA, not the NSA, not the FBI, and the list goes on.
So when the president says he takes exception to any particular clause of any particular bill that he is signing, he takes that exception for all agencies within his power, virtually all agencies of government. When he says the unitary executive branch takes exception to the McCain Amendment, that means no agency of government will be subject to it as long as Bush is president.
I think a better understanding of the effect of this process might be had if we were to look back at something called the "line item veto." Again from Wikipedia, "In government, the line-item veto is the power of an executive to veto parts of a bill, usually budget appropriations. This enables an executive to nullify specific provisions of a bill, rather than only being able to approve or veto a bill in its entirety." Read the rest of this short definition for some background on that concept. It's interesting that the Supreme Court struck down that power when it was given to President Clinton. I had forgotten about that, if I ever knew it. But look at the reason why it was struck down, "that unilateral amendment or repeal of only parts of statutes violated the U.S. Constitution."
Using terrorism as justification, President Bush is using signing statements, the unitary executive concept, and his powers as Commander in Chief to essentially line item veto congressional bills when they are sent to him for signing. That is the legal precedent he and his White House lawyers seem to be trying to establish. Let's hope that somebody brings this issue to the courts soon.