I have various options specified in xorg.conf file for global use across all users and desktop environments on my Linux installation. It look like this:

    Option         "XkbRules" "xorg"
    Option         "XkbModel" "pc105"
    Option         "XkbLayout" "us,ru"
    Option         "XkbVariant" ",winkeys"
    Option         "XkbOptions" "grp_led:scroll,grp:caps_toggle,compose:menu,terminate:ctrl_alt_bksp,grp:switch"

When xfce4-xkb-plugin starts, it updates xkb settings (I suppose via setxkbmap), and resets such options as grp_led, grp:switch, terminate;ctrl_alt_bksp.

So, here is  setxkbmap -print before I start xkb-plugin:

$ setxkbmap -print
xkb_keymap {
	xkb_keycodes  { include "evdev+aliases(qwerty)"	};
	xkb_types     { include "complete"	};
	xkb_compat    { include "complete+ledscroll(group_lock)+ledcaps(group_lock)"	};
	xkb_symbols   { include "pc+us+ru:2+inet(evdev)+group(switch)+capslock(grouplock)+compose(menu)+terminate(ctrl_alt_bksp)"	};
	xkb_geometry  { include "pc(pc105)"	};
};

And after xkb-plugin started:

$ setxkbmap -print
xkb_keymap {
	xkb_keycodes  { include "evdev+aliases(qwerty)"	};
	xkb_types     { include "complete"	};
	xkb_compat    { include "complete+ledcaps(group_lock)"	};
	xkb_symbols   { include "pc+us+ru:2+inet(evdev)+capslock(grouplock)+compose(menu)"	};
	xkb_geometry  { include "pc(pc105)"	};
};

Using version 5.3.3 on Ubuntu Lucid.