This author makes a similar mistake to the ones he accuses prior authors and historians of making. He's pretending as though Bach were operating alone in acting against certain norms in his music. It's obviously preposterous to suggest that anyone is acting alone or making a social statement in drinking to much or fucking hot chicks in the organ loft.
The most common misconception in music history is that it's fairly easy to attribute certain innovations to specific composers. Like, it's often dumbed down and presented as though Bach were the father of tonal music and that he was some kind of music radical in both inventing that system and taking it to its logical extreme.
This is the same kind of over-simplicity that brief histories of science and technology make.
The reality is quite a lot more murky. The tonal system was vestigially present early in the Franco-Flemish school of composition. You can see it forming in the work of Ockeghem and by the time you get to the masses of Orlando de Lassus you get profoundly different work than contemporaries who were firmly rooted in modal traditions like Zarlino and--more notably--Palestrina.
Bach's music is responding to a centuries-old tension between modal, tonal, and chromatic musical elements. Another gross simplification is the idea that modal music slowly evolved into tonal music. That all the modes except for Ionian and Aeolean simply fell out of use. Which is of course absurd since Ionian wasn't a real mode. It was just later included for the sake of theoretical completeness, not a thing composers actually used.
That aside, my point isn't that Bach is acting as a subversive rebel or charting new territory in the way that this author suggests, nor is he a god-like individual of lone genius in the way that traditional historians suggest. He is a part of a movement and incorporates elements from different musical traditions and expands on some of those and formalizes some of them.
The fugue mentioned in the article is more of a musical proof of a mathematical concept than it is an attempt to disrupt norms of melodic writing. The entire point of the Well-Tempered Klavier is to demonstrate that you can perform in all keys without stopping to retune your instrument. The b minor fugue (also weird thing here from this author: it's traditional in music theory and history texts to capitalize major keys and lower case minor keys. In a rigorous paper, this should be written as b minor fugue, not B minor fugue) is a demonstration that even within a single piece of music, you can work your way around the entire chromatic scale without retuning.
On top of that, the author isn't even correct about that particular fugue anyway. Again, Bach is operating in a context and responding to it. One of the main musical consequences of the protestant reformation and the resulting schism from the Catholic Church was that instruments were allowed in religious ceremonies. The "serious" composers of the Catholic church were focused almost entirely on vocal music, and instrumental music wasn't considered very seriously by scholars. But the protestants fostered a movement that was very focused on instrumental music that allowed the kinds of motivic writing that ignores melodic content to a certain extent and enables more intricate counterpoints. There is some aspect of what the author is saying, but it's hardly subversive. It's a continental and cultural and philosophical movement that started long before Bach was born. He's a part of that.
I do appreciate that we should stop pretending that people were pious and holy just because they wanted to be perceived that way and that Bach was way more human than perhaps we're often led to believe. But this author is really, really reaching in this excerpt, and in trying to set the record straight is glossing over all the relevant context that other historians skip over too.