Rights exist as the underlying sunstratum of reasons, principles, and rationales which are never “enshrined into law” by codification or binding precedential case-law, but which are still both necessary for making decisions within any system where shared communal activities are structured by norm-thick concepts like “Law.”

'Reasons, principles, and rationales', seem to me to be the things at the very foundation of reason. I don't see the need to put 'rights' or anything much else below these.

As I've said, if you want to talk about 'moral rights' apart from 'legal rights', that's fine, as long as the distinction is made. The problem is when the two are confused and people talk about moral rights as if they were legally enforceable, which they are clearly not. Napolitano makes this mistake.

The example you give is no more than that of a public official acting within his remit and not an example of 'natural rights' somehow transcending the law. If the judge was to overextend himself and start being creative with the law beyond his license he would certainly be sanctioned by his superiors.