It's obvious that the lyrics are a result of close collaboration by Anno, Wyzgowski, and Sagisu. No, Anno probably don't pen these lyrics in the NTE scores. There are way too many for him to devote that much time and effort into writing such things when he's got to re-think, re-write, and re-render scenes and CGI shots until they feel just right. But these lyrics follow major themes of the films too closely in order for them just to be fluff and stuff in order to pad out the sonic scope of the soundtrack.
Take "The Wrath of God in All its Fury," for example. When taken in context of Beethoven's 9th Symphony and the events taking place on screen at the time each music cue starts, both songs explore the different reactions to 4th Impact's creation of a god. Beethoven's 9th, "Choral," starts when Seele is dismantled before seeing their version of Impact come about. As a result, the music choice is rather joyful, joyful, all ye brethren about creating a god because it's from the point of view Seele. When it negatively effect Misato and the rest of Wille, the music fades into "The Wrath of God" without missing a beat, which is strikingly different in its tone and lyrical message. It shifts from joyfully entering Elysium's sanctuary drunk with fire to a frantic musical explosion with the choir singing about the wrath of God being unlocked in all its fury. This happens because Wille is fearful of this god Seele has awoken.
So, within terms of "Betrayal," we need to ask who's being betrayed and how they're being betrayed. In the movie, the last two lines of the BGM aren't actually sung. It might be a nit-pick, but I think it's important to only analyze what's in the film when discussing the plot points and themes in the film:
Betrayal, in the film, wrote:With vengeance retribution will be sought with time
the sacrifice of the crime
Apostles feed upon the flesh and in return the poor soul reaches out
wrest crippled mental torture the chance to be immortal
The last part is easy. The same word used in the original Japanese dub for Angel is "Shito," which can also mean "Apostle." (Both basically mean "Messenger.") Evas are (presumably in this continuity) derived from the Angels, and we've seen both Angel and Eva use their mouths a LOT when it comes to battle situation. Unit 01 bites Asuka's Entry Plug, Unit 02 bits at the 10th Angel's AT Field, the 10th Angel eats Unit 00 along with Rei, Unit 13 eats the 12 Angel, and Mark.09 bites at Unit 02 Dash's head. (If we include Rei II as an Angel, then we also have her trying to cook meals in order to reunite Shinji with his father. Though Rei doesn't eat meat, so "flesh" is out of the question.) In return "the poor soul reaches out, wrest (= forcibly pulled) crippled mental torture the chance to be immortal." Shinji is being forcibly pulled into mental torture for a chance to be immortal. (Possible clue to the motives behind one of the versions of Human Instrumentality in Eva.)
(Also, fun double entendre, "wrest" is also a key for tuning a piano. Yay, reference to piano symbolisms in Q!)
The first half is the hard part. It starts playing as soon as Shinji scales Lilith's corpse for the spears. Maybe it's just another clue as to what Human Instrumentality is meant to do.