Perhaps given Gnome HIG says "users must use Adwaita, they are not to be allowed to make any choices" they think thats a solution [end grumpy olde guy rant]?
AFAIK that's indeed the "solution": disallowed theming. IIUC to the extent where libadwaita (a broadly used GNOME UI library) overrides user choice.
I don't like that myself, but I don't know of an actual solution to the problem, as the app can't provide tailored support for all themes, and theme authors don't have tailored support for all apps either.