Congress certainly can't regulate the substance of how the courts apply the law, that's absolutely true. But they can regulate the procedure of how courts apply the law, and as per the examples I gave, they have often done so, including against the Supreme Court's wishes. (The two examples I gave are the Rules Enabling Act and its amendments, controlling how the Supreme Court manages the federal rules for both criminal and civil procedure, and the handling of the Federal Rules of Evidence.)

I'm not disagreeing with the other examples you gave, including about original jurisdiction - clearly separation of powers and the constitutional structure are both real and binding. But equally, those concerns don't prevent the kind of personnel regulation we're discussing.