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If /etc/xdg/autostart/foo.desktop exists, the Session and Startup Autostart tab shows that item in the list but does not allow editing or removing it. Ideally it would (with any edit creating a copy of the file in ~/.config/autostart and putting the edits there), but that is more of a feature request than a bug.

If /etc/xdg/autostart/foo.desktop and ~/.config/autostart/foo.desktop both already exist, then xfce4-session correctly uses ~/.config/autostart/foo.desktop and ignores /etc/xdg/autostart/foo.desktop at startup; however, the control panel still refuses to edit ~/.config/autostart/foo.desktop, which it should allow (though if the override mechanism is not properly implemented, it should probably still disable the remove button); it seems like a bug to me for this to not work since the actual editing mechanism is the same as for personal-only (as opposed to personal-override) autostart items.