App Icons are the identity of an app. Changing an app’s icon denies the developer the possibility to control their brand.
FOSS is built around the principle of software being free, as in freedom. If you want to restrict how a user interacts with your software for the sake of a corporate identity, fuck right off and go to an Apple platform. We won't miss you.
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.
Oh no, how tragic. Your application doesn't look like your screenshots when running on my customized system. You know what would be more tragic? Your application sticking out like a sore thumb.
User Help and Documentation are similarly useless if UI elements on your system are different from the ones described in the documentation.
I'm really struggling to understand their perspective here. Is their documentation really that bad, to the point where it would be impossible to follow if the background color is wrong or if the buttons look like slightly-different buttons?
The only reasonable complaints they had are with broken styling or icon sets replacing icons in a way that changes their meaning. The rest of this is just straight up stupid.