Earlier quoted context omitted.
Seems like you didn't actually read the linked "stop theming our apps" page. They have no issue with users theming their own systems, and gnome apps are still themable. Developers have an issue with distributions shipping a custom theme by default, which breaks things and causes users to report issues which aren't the fault of the developers.
Distributions are operated by users. They're basically just a collection of recommended packages, curated by the distribition maintainers. Why should users be prevented from sharing their preferred themes with other users, in the form of distributions? Besides, if app developers are doing their job properly as described in the parent comment, then neither user themes, nor distribution themes, should break anything.
Because when a distribution like Ubuntu ships a broken theme, and some app doesn't work as intended, users will report this to the app although it's a bug in Ubuntu.