I was commenting from the general point of view of the Blackstone of Military Law, William Wintrhop, who said the President is the original source and authority for military regulations. Just stands to reason that a CinC with compromised authority compromises the chain of command.
If one does not read the Constitution one might come to that conclusion based on the President being CinC. If one reads the Constitution, specifically Article I, Section 8, then it's clear that that conclusion is wrong. Congress is the source and the authority for military regulations and military law.