When developing Gnome in July 2019 it came to my attention that the settings I had created and saved in ~/.config/dconf/user were not applied into the system.
Updates came in /etc/skel/.config/dconf/user.
We did the skel command (check your aliases) but the new settings like icon, wallpaper, themes, …
Dconf is a kind of database that keeps track of all the settings of Gnome. You can only edit it via dconf-editor.
Copy/paste the /etc/skel/.config/dconf/user manually over to ~/.config/dconf/user
and check and recheck