As I said in other threads before, once you get the narrative of Illumination Theory, the middle section would make a lot of sense.
Live, Die, Kill posed earthly problems by asking the questions, what are you willing to live, die and kill for? It is unenlightened, unilluminated, so there are no answers yet.
The shift to the ambient section refers to a transfer from the earthly plane to a transcendental plane. It is marked by the shift from a relatively "noisy" musical atmosphere to something more reflective. The ambient section is lengthy, which I find as purposive to indicate that illumination or enlightenment does not come easily even in a moment of transcendence. But enlightenment slowly creeps in with the slow build-up of the orchestral music. Illumination is reached when the orchestra reprises the intro music from the Paradox of the Black Light section, which marks a new beginning, the difference being that this is already an enlightened one. So in contrast to Paradox, the orchestral intro is brighter, more positive, more enlightened.
After the moment of enlightenment, the song goes back from the transcendental plane to the earthly plane. This is marked by the shift from the reflective music of the orchestra to the "noisy" musical atmosphere of the real world. However, unlike Live, Die and Kill, the Pursuit of Truth section now gives answers, not questions. Which is why this is in the Illuminated half of the song.
Does the middle section kill the momentum of IT? If you do not care about the narrative, the story that the song is trying to tell, it would sound that it does. If you do pay attention to what story the song is trying to tell, the middle section makes a lot of sense. There's nothing superfluous about it at all, to the point that even the length of the ambient section makes sense.
About reprisals, IT is all about reprisal. It is about mirroring. The first section is a paradox with a dark atmosphere, the end section is a paradox with an enlightened atmosphere. The riffing section that bridges the initial paradox to the questions of Live, Die, Kill is the same as the riffing section that bridges the answers of the Pursuit of Truth to the ending paradox. The questions posed in Live, Die, Kill are answered (thus, reprised) in the mirroring section of the Pursuit of Truth. The unenlightened ambient section is mirrored by the enlightened orchestral section. The unenlightened overture in Paradox of the Black Light is reprised in an enlightened version in the orchestral section of the Embracing Circle. The song starts with a crescendo drum roll, and ends with a decrescendo drum roll. Even the lyrics of Surrender, Trust and Passion reprises each other within that small section.
I don't see how you can get any more reprisals than that within a 20-minute song. Even Octavarium does not have that perfectly mirrored structure, and that one talks about going in circles.
IT is not a song about momentum. It is a song about gaining enlightenment. Maybe it can kill momentum in a live setting, but that is not what the narrative of IT is about. It was composed to tell a story.