I would heartily agree that an Emperor or someone carrying an Imperial Warrant has essentially unlimited power over all Imperial institutions including the military, the ministries, and the nobility. An Emperor could certainly command an archduke, admiral, or the Minster of Justice to carry his luggage anywhere, and I would assume this authority would extend to any Imperial citizen on board an Imperial ship or occupying an Imperial facility.
I don't believe there is any example in Agent of the agent having direct legal authority over planetary governments or citizens while on their sovereign world.
Back to Article 1 - "The Imperium considers as citizens any living recognized sentient creature native to or naturalized by a member world of the Imperium, or any living recognized sentient creature swearing fealty to the Imperium directly."
The sovereignty of a world exists only where it does not conflict with Imperial Law, which is embodied in the word and person of the Emperor (or his designates). The governance of worlds is at the mercy of the Emperor because he can create any law he or she wants and the only recourse of the Moot is to dissolve the Imperium if they don't like how things are going. The Emperor can create and dissolve entire organizations at will in order to enforce "Imperial will" not, significantly I would suggest, "Imperial law".
The issue is not if the Imperial will trumps individual or planetary sovereignty, the point is that the Imperium has decided that it is more efficient for individual worlds, when travel is at the speed of jump, to govern themselves and has set that up as the default for membership - except where Imperial interests trump local ones.
If you read Article VII it has more verbage about starports and like areas of extra-territoriality are bastions of Imperial power and authority - rather than a discussion of how Imperial power is limited there. In fact, in combination with Article IV, I expect arguments have been made that *any* restriction of access to the starport/startown is a restriction of free trade - probably with counter-arguments that "members" refers to worlds while citizen refers to individuals, blah, blah, blah...
Again, local and individual sovereignty exists at the mercy of the Emperor not in spite of or in challange to the authority of the Emperor.
That might not be pretty or palatable to 20th century political morals or ethics, but the Warrant of Restoration is pretty black-and-white when it comes to enumerating rights and powers.
There is an individual right to freedom from chattel slavery and to citizenship.
There is a member's right to free trade and a freedom from piracy and smuggling (the latter important because it supports the general sovereignty of member states to 'run their own house')
There are general right's to a common standardized currency, standards of measures for trade, and a single measure of time.
Nobles have the right to sit on the Moot which in turn has the right to confirm the Emperor on ascension, and to dissolve the Imperium if they choose.
There is an implied but not well delineated right to the rule of law - but where it is clear that the Emperors will is the foundation of said laws.
D.