This novel discusses actual torture, so the titular Question is obviously the question for intelligence that the French government wanted him to answer, right? Not exactly. The real Question is the issue of torture. In a strange way, the question of torture is theological in nature, because it seems to stand at odds with the sovereignty of the human soul. By torturing Alleg so brutally, the real Question is whether humans have the right to torture information out of other humans.
When he describes struggling to breath because of the French waterboarding him, the description is genuine and confused. He doesn't even know what waterboarding is—this happened a long time ago, after all, so when he describes the feeling of dying and drowning through his gasps for air, he means he literally believed with his entire being that he was indeed dying. The question is clearly about the threat not of pain, but of death. Clearly, the French have no care for the value of his soul or life, but rather, they only keep him alive to exploit him of his knowledge.
The battle against Pentothol is perhaps the most difficult passage of the book, because it exacerbates the problem of torture. Pentothol removes agency from a person, such that when asked a question, they will answer it truthfully, because their brain has been chemically altered to the desired effect. That's what torture really amounts to, at least in Alleg's case, because whether through Pentothol or pain, the goal was clearly to change his experience of reality until he cracked under the agony of true torture. This begs a moral-theological Question about the nature of reality, and whether humans have the right to induce such abominable experiences of consciousness.