"He doesn't know the sentence that has been passed on him?" "No," said the officer again, pausing a moment as if to let the explorer elaborate his question, and then said: "there would be no point in telling him. He'll learn it on his body." (12)
The penal colony's use of the apparatus is based on this idea that the prisoner somehow learns something through his body and its wounds that he does not learn by merely being told. It's as if real learning, or understanding, can only come through suffering – it can't just be intellectual.
[The officer:] "Of course, the script can't be a simple one; it's not supposed to kill a man straight off, but only after an interval of, on an average, twelve hours; the turning point is reckoned to come at the sixth hour." (16)
Merely killing or punishing is not the point of the apparatus. The suffering the condemned man undergoes is supposed to bring about a transformation in him, and this requires that it last for quite a while. The long length of time calls to mind numerous elaborate ritual sacrifices or punishments, not the least of which would be crucifixion (if you wanted to read this as a religious allegory).
[The officer:] "The first six hours the condemned man stays alive almost as before, he suffers only pain. After two hours the felt gag is taken away, for he has no longer strength to scream […] Only about the sixth hour does the man lose all desire to eat." (16)
In the process of suffering under the Harrow, the prisoner becomes incredibly weak and basically loses his vital functions, his ties to life. In the last six hours, his attention can be concentrated entirely on what is being painfully inscribed on his body – his concentration will be entirely on his suffering. That's the point.
[The officer:] "But how quiet he grows at just about the sixth hour! Enlightenment comes to the most dull-witted. It begins around the eyes. From there it radiates. A moment that might tempt one to get under the Harrow oneself. Nothing more happens than that the man begins to understand the inscription, he purses his mouth as if he were listening. You have seen how difficult it is to decipher the script with one's eyes; but our man deciphers it with his wounds." (16)
This is where the officer first talks about the prisoner being "enlightened" (and also foreshadows his own act of going "under the Harrow"). But of what does the prisoner's "enlightenment" consist? In the most obvious sense, he just begins to figure out what it is that's being written on him, and presumably only reaches complete "enlightenment" when he knows what's being written on him. But there's got to be more to it than that…right? Some special meaning is clearly attached to the idea that the condemned man learns through his wounds. Is it only this way that he begins truly to feel that he's broken a commandment, to experience his guilt?
[The officer:] "You may want to interpose that you never said any such thing, that you never called my methods inhumane, on the contrary your profound experience leads you to believe that they are most humane and most in consonance with human dignity, and you admire the machine greatly – but it will be too late." (25)
Although the officer is speaking hypothetically of what the explorer might think here, it seems pretty clear that this is what he, the officer, does think. It's interesting that he would say his methods are "the most in consonance with human dignity," since this seems exactly what they're not. The officer's methods publicly subject a naked human being to unimaginable pain as his body is destroyed. Is the officer just crazy? Or does he have a reason for saying this? Perhaps he believes that the capacity to suffer, and through suffering to learn, is the most dignified thing a human being can do…
And here, almost against his will, he had to look at the face of the corpse. It was as it had been in life; no sign was visible of the promised redemption; what the others had found in the machine the officer had not found; the lips were firmly pressed together, the eyes were open, with the same expression as in life, the look was calm and convinced, through the forehead went the point of the great iron spike. (46)
The officer is in the end denied his own hope to experience the "transfiguration" of torture under the Harrow. Note the word "redemption" here. That suggests that perhaps the point of the suffering is a sense of having redeemed one's guilt – by suffering, you've somehow rendered yourself guiltless, perhaps? If you do believe that all people are guilty, as the officer seems to, the promise of redemption from that complete guilt, not just the guilt of the particular crime you committed, might be very powerful – if indeed such a redemption is possible. The officer never finds out himself, though he believes in it. Since the explorer, and the reader, only know of it through the officer's (possibly colored) description of past executions, neither do we, really.