To fully understand how all this works, you have to understand the cyclopean beaurocracy of the Imperium of Man. Think about how Inquisitors operate. The Inquisitorial Remit gives the Inquisition the power to act as a self governing body answerable only to itself and the God Emperor of Mankind. This gives them authority that rises even above the central governing body of the Adeptus Terra itself. This gives each Inquisitor tremendous power that, officially speaking, not even a High Lord of Terra can refuse.
The key phrase here is 'officially speaking'.
In reality, there are multitudes of overlapping authorities that turns Imperial governance into a contradictory mess. Inquisitors have the official authority to investigate powerful members of the Adeptus Mechanicus, the Novis Nobilite, or the Adeptus Astra Telepathica, but remember that the very function of the Imperium relies on these organizations. Thus, these indiividual organizations all have incredible amounts of leverage and power in their own right. In addition, the order of one Inquisitor can come into conflict with the order of another, and the same is true of whole Ordos or Conclaves of Inquisitors. Though some might disagree, I have personally always considered the Imperium to be a very specific statement about the nature of political beaurocracy in the real world. Multitudes of agencies all given extreme authority that often overlaps and conflicts. Two Inquisitors can consider each other heretical, go to war with one another, dragging millions and millions of soldiers from multiple planets into the conflict, and neither one is doing anything illegal.
Then we focus on the crux of this forum and post: Rogue Traders. The are legally given the authority to act outside the bounds of Imperial Law. Think about that for a moment: The legal right to act illegally…This is an inherent and intentional contradiction, just like everything else in the Imperium. It functions much like the way espionage works in the real world. If you think about it, a spy is legally impowered by his government to break international law. The spy acts on behalf of his government, but if he gets caught on enemy territory he is the one responsible for getting himself out of it. His government will not intercede if he gets caught breaking a law that his government cant afford to get caught breaking.
In the end what this means is that a Rogue Trader has the authority to break the law, but he alone is responsible for inforcing that authority. The Warrant gives him the power to deal with an Inquisitor as a peer. On the surface this means they have equal authority, but the question is who has the most influence and power? Is this Inquisitor acting alone, or on behalf of a greater conclave? Is the Rogue Trader acting alone, or on behalf of a vast and powerful Dynasty that the lone Inquistor doesn't have the resources to deal with?
Things in the Imperium are never simple.