> Shouldn't that require a Constitutional Amendment?
No, Article III § 1 explicitly vests judicial power “in one supreme Court, and in such inferior Courts as the Congress may from time to time ordain and establish” [1].
> Why isn't the investigative/prosecutorial branch distinct from the executive and judicial branches though?
No, to change the separation of powers they need a constitutional amendment because that's a change to the Constitution, and amendments are the process for changing the Constitution.
To interpret what was meant by Liberty and Equality as values, as a strict constructionist.