It seems like you’re thinking about “customization” as “customizable look and feel”, but “desktop customization” goes way beyond than that.

They should just talk wayland directly. Using GTK just for desktop integration is not what GTK is for. The friction will only increase over time.

I recall reading a comment from (allegedly) a Gnome dev on Reddit a few years ago saying that Mozilla should port Firefox directly to Wayland (?) so to make it toolkit-agnostic.

I don’t know if that is actually a possibility, but that would be great. You can’t use Firefox if you don’t have GTK installed, not even an appimage of it - but apparently you can get stuff like Inkscape running without it just fine:

https://github.com/srevinsaju/Firefox-Appimage/issues/15