Você pode definir / desabilitar os atalhos programaticamente, usar o dconf no modo CLI, conforme explicado aqui
Exemplo:
# remove annoying ubuntu shortcuts
dconf write "/org/gnome/desktop/wm/keybindings/switch-to-workspace-right" "['']"
dconf write "/org/gnome/desktop/wm/keybindings/switch-to-workspace-left" "['']"
dconf write "/org/gnome/desktop/wm/keybindings/switch-to-workspace-top" "['']"
dconf write "/org/gnome/desktop/wm/keybindings/switch-to-workspace-down" "['']"
Execute esses comandos na inicialização