After users changed the font in one location, we told them there was another place to change fonts in the Control Center. Depending on time, we either let them explore to find the other location or guided them to it. We had them change the font in this second location and pointed out that not all the fonts on the screen had changed. We then told users that there was a third location to change fonts. That's cumbersome, I wouldn't like that.
Users expect to go one place for fonts, make one change, and have it apply to the whole desktop.
The fonts example illustrates how users will become frustrated if the underlying software does not support their mental model. If a user's mental model is that changing fonts happens magically, then we have to design to that model. We can't burden them with the distinction between fonts in the window manager, fonts in the current selected theme, and fonts inside Nautilus themes. We can't let the development process, of componentized, modularized pieces coming from different origins, permeate up to the user's level. The icons are big and easy to see.