I read this statement by Bolten in the FT article titled "Cheney the survivor without challengers", and it sounds to me like he thinks separation of powers is something like, I can do whatever I want.
Mr Bolton says on foreign policy the Bush administration will retain its strongest freedom of action. "People tend to forget that we do not have a parliamentary system - the powers of the executive do not depend on who controls the legislature or on the state of public opinion," he says. "We have a separation of powers. This is especially true of foreign policy.http://www.ft.com/cms/s/0/0b44ff52-5823-11dc-8c65-0000779fd2ac.html