To massively oversimplify, the Japanese religion of Shinto contains many principles concerned with flowing water and purity. According to Shinto, your actions should mirror the properties of flowing water, for water which flows is pure. Conversely, water that stagnates becomes polluted - a breeding pool for impurities such as parasites and disease. It is a source of illness, or as the Archangel equates it, “distortion”.
Several items and concepts in Baroque reference these principles, such as the Waste Water item or the "pure water" Eliza seeks. Waste Water is described as "corrupted water", or more literally, "kegare water". 'Kegare' is a Shinto concept pertaining to a type of impurity that stains the very being of any person who comes into contact with it. This impurity often spreads via liquids that have ceased to flow (such as spilt blood). In game, ampoules filled with this stagnant Waste Water will make you weaker, but will make Grotesques stronger. This is because their delusions have caused them to reach a state of total emotional stagnation. It’s no coincidence that this stagnation breeds in the absence of motion-inducing chemicals like noradrenaline (which was removed from God in order to drive her mad). Adding more stagnation in the form of Waste Water makes these delusional, stagnant creatures even more distorted, and therefore more powerful.
In the PS1 port, the Coffin Man comments that there is "no pure water left in the world". As the player can clearly see, all the water outside has turned a sickly, stagnant green. Considering that Eliza and the Mind Reading Thing both confirm that the world itself is God's language, this means that water is the flow of information through the world. Fitting, as water comprises the majority of all living beings and is the source from which all life originally evolved. With the lifeblood of the planet having stagnated in this way, it is no wonder that the only wildlife that seems to have survived the Great Heat Wave are a variety of large parasitic worms. Even time itself has stagnated, as the protagonist finds himself locked in an endless cycle of death and resurrection with his dead twin.
Shinto traditions have fueled a lot of casual discrimination in Japan’s cultural subconscious (such as depicting women as sources of impurity), and it is not uncommon to see these bigoted tropes in other Japanese videogames and media. Baroque may make liberal use of Shinto in order to further illustrate concepts central to its plot, but the moral of the game is a complete rebuttal of what Shinto preaches. The game’s twist ending refutes these concepts so entirely that the game’s message could easily be read as a rejection of Japan’s historically prejudicial views towards disease and disability.
In Japan (and many other places across the world), sickness and abnormality in all forms were traditionally viewed as something to be hidden away. People were expected to suffer quietly, out of the public eye.The influence of this societal prejudice can be seen in the 2016 Sagamihara tragedy, in which a man killed 19 people and injured 26 others at a care facility for the disabled. The killer envisioned a world in which the disabled were euthanized, as to lift their ‘burden’ from society, and that such killings were “for the sake of Japan and world peace”. Despite occurring almost two decades after the release of “Baroque”, his motivations are chillingly similar to those of the Archangel. Both want to eradicate those they view as “distorted” in order to purify the world. But as we learn in the game’s finale - “Trying to purify the world [is], in itself, a distorted delusion.”
The term "Baroque" originally referred to a type of pearl. This is likely why Idea Sefirot closely resemble these gemstones. However, they also serve as an analogy to Baroque’s central moral, as pearls are formed around impurities. The impurity is an integral part of the pearl and not something that can be eradicated. Distortion - whether it be disease, disability, or even the delusions we form to cope with suffering - is a natural part of our world and is present in each and every one of us. As Urim and Thummim put it, “Everyone is distorted, so I think it’s a mistake to condemn anyone over their distortions.”
Design documents confirm that “sick people” was a central theme in the game’s plot. This is the reason for so many of the character costumes including elements like bandages, gauze, and medical tubing.
The retroactive addition of the Archangel’s infirmed sister in the PS1 port also draws from traditional prejudices against the sick and disabled. The Archangel in this revision is lashing out against this exact societal bias, as it led to his deformed sister wasting away in a dark room out of view from the public. It makes him a more sympathetic character, but inadvertently vilifies the cause by associating it with the PS1 Archangel’s petulant, immature, and violent desire to get even with society.
The 2007 remake further erodes the game’s messages about ‘not averting your eyes from distortion’ by redesigning the cast to be more conventionally attractive and commercially viable. Once ambiguously female characters are made more obviously feminine through redesigns and soft-spoken voice acting, deformities are downplayed in favor of generic anime aesthetics, and many mentions of physical violence or death have been scrubbed from the script.