The file is ~/.config/gtk-3.0/bookmarks and according to https://docs.gtk.org/gtk3/class.Settings.html /etc/xdg/gtk-3.0/bookmarks should be the system-wide path. But it doesn’t work.
I do not see any mention of bookmarks being considered settings.
Checking the source code, Nautilus only looks at the GTK 3 bookmark file inside XDG_CONFIG_HOME/~/.config. Plus the legacy one in the home directory:
GTK itself does the same:
Oh, got it, thanks! So Nautilus just uses the GTK setting directory for bookmark but doesn’t use the system-wide path.