The vows the Penitent One and Crisanta take are somewhat symbolic if you consider the events of the game. The Penitent One has taken a vow of silence, choosing not to speak or say anything. The Penitent One becomes the new figurehead of Cvstodia's religion, but without giving any words to help lead the faithful, they will simply keep indulging in their Martyrdom Culture, keeping the place as a Crapsack World. Likewise, Crisanta's vow is that she's given up her sight, but this doesn't impede her whatsoever. She's so blinded by her belief that the Grievous Miracle is righteous and anyone who would oppose it must be evil that in the good ending, she seemingly undoes the Penitent One's sacrifice just to start the cycle of pain and misery brought on by the Grievous Miracle.
The steps the Penitent One has to take in order to achieve the game's best ending make more sense when you consider what his ultimate goal really is. In seeking to end the Age of Corruption and break the cycle of suffering the people of Cvstodia are trapped in, the Penitent One is essentially trying to become a Messianic Archetype; however, since the religion of Cvstodia is a very darkExpy of Roman Catholicism, it would perhaps be more accurate to say that the Penitent One is trying to emulate Jesus specifically. As such, atoning for his sins alone (whatever they may be) is insufficient to achieve the Penitent One's goal — he has to atone for everyone's sins, or at least as much sin as he possibly can, by destroying the Confessor statues and harvesting the Guilt they contain. This is best shown in that, after the Penitent One has destroyed all of the Confessor Statues and taken all of their sins, the thorn in Mea Culpa has evolved into the "Cvstodia of Sin", implying that the Penitent One has taken all of the guilt of the people onto himself.
Why does the Penitent One die in the new Wounds of Eventide ending? Well, there's two possible explanations for this. The first is that, if the Penitent One managed to destroy the Miracle, the thing that's kept him alive and revived him through the many deaths a player will experience in game, he would naturally die as when it leaves, the power keeping him alive will also fade. The second explanation is that, if the Penitent One only destroyed the High Wills but not the Miracle, it's likely he died simply because his quest and his penitence, ending the Grievous Miracle or its hold on Cvstodia, was over and his job is done. Supporting evidence for "dying when one's penitence is done" comes from various penitents who either died or ascended towards the Dream, including but not limited to: Redento, Socorro, Jibrael, Nacimiento, Soledad, and potentially a few of the bosses if Deogracias' mention of them being released from Penitence when beaten is taken into consideration.
The game's title itself. From a Christian perspective, the idea of an entire religeon (or, rather, a cult or extremist denomination as implied by flavour text) dedicated to suffering for the Faith, not because of the hatred of the nonbeleiver, but because a sadistic deity demands his worshippers hurt themselves to show how sorry they are is blasphemous. Even the act of self-flagellation is a twofold blasphemy, as it's both witchcraft ("cut not thy bodies for the dead") and an attempt to earn salvation through works rather than receive it by faith (My grace is sufficient for thee). However, from the Cvistodian perspective, the idea of God as a loving father who weeps at our suffering and forgives at request is.
Defeating the final boss is denounced as Basphemia Maxima (highest blasphemy). But the final boss isn't God, but the pope. His (un)Holiness Escribar himself committed Blasphemia Maxima by placing himself above or equal to God.
Fridge Horror:
The Flavour Text for the bone of Victor Hernandez mentions that he had been accused of heresy due to the fact that he went out into the world as a missionary to "civilize" the Barbaric tribes, only to come back and say that Cvstodia was far more barbaric than anywhere else he had been to, that implies that Cvstodia is the only place affected by the "Miracle" rather than the world at large, and the rest of the world is either apathetic to their suffering or at least scared of interfering in case the Miracle decides to notice them.
Alternatively, since it isn't clear whether the people the Ossuary bones belong to died before or after the Miracle, it could be a sign that Cvstodia has always been a brutal theocracy and the Miracle simply made things worse.
