The author presents valid and sensible issues with the state of theming on the GNOME platform. And the overarching topic is essentially User Experience.
Even the slightest change in color can introduce friction between UI elements. Or to be more extreme, if a theme turns your entire app into a white blurry mess, you would get mad at the application, and not the theme. Although many of the same design principles are used in the making of either a chair or a graphical user interface, they are definitely not the same in any regard.
On the topic of icons: just like language, they evolve over time. On top of that, icons can have different meaning depending on your background. Icons can be combined to form a composite icon, and now imagine one of those icons is not displayed as you intended it to be. The entire meaning can change because the design intentions are lost.
On the topic of branding: it's not about your desktop being a billboard. It's about being able to recognize the brand across different operating systems, and it's also - more or less - the only thing about the product that is not designed for the purpose of user experience (but in a sense, they still are). And let's be honest: most apps we use in our day to day life have very tame brands and adhere to certain standards. That is because the apps we use are usually good, and we throw the bad, obnoxious ones away really quickly.
All in all, the author presents valid concerns, especially if you don't project them on how you prefer your UI, but rather, how potential Linux / GNOME users could have additional difficulties because of theming issues.