In the gnome-wm script, the following cases handle compiz/beryl:

case `basename $WINDOW_MANAGER` in
  compiz)
    export LIBGL_ALWAYS_INDIRECT=1
    gtk-window-decorator &
    OPT3=glib
    OPT4=gconf
    ;;
  beryl)
    emerald &
    ;;
esac

With compiz-fusion, compiz should now start with a single plugin, ccp, which loads the configuration from whichever config backend the user has chosen, with gconf being the default in Gnome. Using the gnome-wm script in its present state will cause compiz to start with all user configuration ignored entirely as there is no longer a gconf plugin. Also, a user can choose to use the flat file config backend instead of gconf even under Gnome.

The config for the decoration plugin can also start the window decorator, so for distros shipping compiz populating the default decorator in the compiz config makes more sense than starting it here. Also, users might choose to use the emerald decorator with compiz under Gnome, even though it does not respect Gnome themes the way gtk-window-decorator does, because of the extra bling it provides.

Finally, beryl has been replaced by compiz-fusion, so you should drop beryl entirely from this file.