I wasn't actually thinking about Imperial Warrants. Consider an Imperial Navy Captain who knows a liner is carrying passengers infected with space plague. He decides that preventing the liner from ever landing and allowing the plague to spread is in the interest of the Imperium. He decides to destroy the liner and all on board. The act is harsh, possibly an over reaction and probably wouldn't go down well with the relatives of the passengers and ship owners. The Imperial view however would be that the Captain has taken appropriate steps to safe guard the Imperium and after a perfunctory court of inquiry the Captain would be back to duty.
You're confusing authority with license. An Imperial captain far from any superiors has the authority to decide how to handle a crisis. That doesn't mean he isn't constrained by law. There's the Imperial Code of Military Conduct to begin with. I disagree about the probable reaction of his superiors, but the salient point here is that
if they choose, they can bring him before a court-martial. That very act means that he is subject to the law. If he was above the law, he could wave his commission and tell the court of inquiry to go kiss his hand.
Now compare that to the Space Pirate who scuttles the liner he just robbed. That act is against the safety of the space lanes that the Imperium is meant to enforce. The Space Pirate will be subject to the full force of the law.
No, compare that to the Imperial Navy captain who plunders a liner. If the captain truly is above the law, no one can call him to account for such an action.
What I am saying is that in the Imperium justice is not blind. The people in charge may choose to apply the law or to give a "free pass" when the result of an illegal action benefits the Imperium.
But that's entirely different from being above the law. Even in societies with all the constitutional safeguards you could possibly ask for, the executive usually have the power of amnesty. (Which is, incidentally, one of the few powers we have direct canon evidence that dukes have).
Your captain would IMO be found guilty by a court-martial but, due to the unusual circumtances that so richly justified his action[*], with a recommendation of clemency.
[*] Do please note how manfully I've struggled not to quibble about your example. 
The OTU has no constitution.
Neither does the UK.
The law is based on Imperial edicts and treaties between the Imperium and its member worlds.
So it is. But there is a law.
Traditions such as the Right of Assassination can trump the law.
By the Classic Era the Right of Assasination had not been invoked for 500 years. It is so much off the books that potential claimants are allowed to carry loaded guns into the Emperor's presence and the half of the bodyguards that weren't in on Dulinor's scheme were taken so much by surprise that not a single one of them managed to get a shot off before being gunned down. And what's more, Dulinor was prepared to bet his life that they would be so surprised that none of them would get off a shot.
The Imperial Rules of War are an example of the broad principles the Imperium applies to the regulation of conflict. With 11,000 worlds it would be impossible to legislate for every possible legal requirement so the Imperium defines broad rights and responsibilities for its member worlds and sets up its own government to regulate narrow areas of responsibility, such as commerce, improving technology, colonization, information & communication, and high justice.
The Imperium has legislation to give its servants broad authority, yes.
Its not a poorly organized place, it is a very big and diverse place which requires a lot of personal responsibility and initiative.
Agreed, but that's not at all the same thing as Imperial officials being above the law.
Well spotted but you misunderstood my intent in using the quote. I said this can be written. There is no limit on Imperial power, the Emperor is sovereign, all power emanates from him. If the emperor chooses to invest part of that power in an individual he can. Edict 97 tells us that everyone is to assist the holder of an Imperial Warrant with all the power they can bring to bear.
When 34 pages, even 34 pages of legalese, are boiled down to one sentence, I think it's a fair assumption that a few nuances would get lost in the process. I think this is what the man on the floor is expected to do when presented with a warrant. I also think that it is the right and duty of Imperial high nobles and high-ranking Imperial officials to prevent the bearers of warrants from abusing them, and that in doing so they would have Imperial laws to guide them.
The wisdom of Emperors is an unknown quantity. There is nothing to say that an Emperor might issue an unlimited warrant. Even an "unlimited" still comes from the sovereign so the Emperor remains a final arbiter of whether something has been "done for the good of the state". Bearer warrants do appear in Traveller, again the Imperium is a big place, it could take up to a year for the Emperor to identify a named individual on the borders and issue him/her with a warrant. It would be easier to send a bearer warrant with an official who could identify a worthy recipient. Making bearer warrants unlimited is a bad idea, but Emperors are not immune from bad ideas.
And said warrant would be made out to bearer but have a blank spot for a name for the official to fill in, being invalid until and unless it was filled out and signed by the official. At least, that's how I think anyone with two brain cells to rub together would do it.
Hans