Your perspective is more clear now. But I disagree.

The article was not about Mutter exclusively. It explained Mutter dropping X11 made GNOME strictly focused on Wayland-based environments. And GNOME Shell would be tied to Mutter even if the article didn't mention it.

Mutter is a library. GNOME is not the only desktop environment which uses it. I don't know if the Pantheon developers wanted to drop X11. But Mutter dropping X11 imposes this limitation on Pantheon.

Your claim the Transmission discussion was not about GTK was incorrect by the way. The GNOME developer said they hadn't decided if GTK would deprecate GtkStatusIcon. The Transmission developer requested GTK make an abstraction. The last comments were a GNOME developer recommending Transmission change architecture so it could support GNOME and in his words whatever odd desktop people want to use after GTK deprecated GtkStatusIcon.

Libraries and applications are not separate inherently. Apple's application scripting architecture was a great strength when it was more supported for example.