Bugs are bad, yes.
> Icon Themes can change icon metaphors, leading to interfaces with icons that don’t express what the developer intended.
That is not a problem if you use icons for the purpose they are intended for.
> Changing an app’s icon denies the developer the possibility to control their brand.
Good. My computer is not your billboard. Consistency is more important than your "brand".
> Appstream Screenshots (the screenshots used in GNOME Software or Flathub) are not very useful if they look nothing like the real app does once you install it.
> User Help and Documentation are similarly useless if UI elements on your system are different from the ones described in the documentation.
Nonsense. Theming doesn't affect the layout of a program. If people were that bad at abstraction, then how do they recognize they can sit on a metal chair if they are familiar with wooden ones?
> They are built and tested for the upstream GNOME stylesheet, icons, and fonts, so that’s what they should look like on peoples’ systems.
No. They should look like the user chooses them to look. One way for the user to express their choice is to choose a distribution whose theme they like.
> Changing third-party apps without any QA is reckless, and would be unacceptable on any other platform.
∀x. x without any QA is reckless.