While I have no authority to say that a ref's calls could ever be wrong, even the brightest people make honest mistakes. I think that it's less of a challenge of authority, and more of a question of accuracy and reliability. The rules should be upheld, and if a rule has obviously been violated, and no penalty been attributed to the 'perpetrator', I think challenging is perfectly appropriate.
I believe the intention of 5.5.3 is to say that 'should a ruling be difficult, or there be no correct answer, the ref's word is law,' rather than 'the ref can choose who to assign penalties on a whim' or 'despite human error the ref's word is more important than what actually occurred.'
I meant no offense to anyone who has been or is a referee, and all of my examples were meant to be hypothetical and unrealistic
