If we go back to your initial comment, you started with a strawman criticism. You said, "It seems as though you are saying that there is no such thing as harmony."
What I say in the article, rather, is that "the problem is that the harmonies in question are all hallucinatory, as is made clear precisely by what we call the modern skepticism that trades our small-minded happiness and self-assurance for dehumanizing knowledge of the world’s monstrous inhumanity."
Of course, harmonies (pleasing relations) exist. They exist foundationally, or most literally, in music, and the ancient Greeks showed that mathematical patterns underlie the pleasing musical tones. By extension, there are non-musical patterns that please. For instance, as you say, some romantic relationships work while others don't.
The more extended the sense of "harmony," though, the more strained or weak the metaphor. Metaphors are strong or weak depending on the amount of posited similarity. People can be pleasingly related, like a harmony of musical tones, because people are playing the same tune, as it were. People are members of the same species, the way certain notes belong to the same scale.
The problem arises when we speak in the most strained way about a pleasing relation between people and nature. This likely originated from Kepler's occult talk of the "music of the spheres," so Vervaeke's emphasis on cosmic harmonies may rely implicitly on that figure of speech or dubious bit of metaphysics. At least, in his case it's based on Neoplatonism, which projects certain personal qualities onto impersonal nature.
The more different nature is from people, the more dubious the talk of any harmony between them. If some such pleasing relation remains, it will be purely subjective, meaning it will depend on what you find pleasing.