I am using xfce4-power-manager but wondered why every time I logged in, gnome-power-manager would still start. I also noticed that it was in the Autostarted Applications list, and would disable it. I would be unable to remove it. Alas, it would be re-enabled. If I deleted it from ~/.config/autostart, the file would be re-added. It seems that it is referenced in /etc/xdg/autostart. The system should give some hint that setting reguires root access to remove/edit, and give the option to gksudo in order to edit it, instead of leaving it disabled.
No, this is correct behavior. System-wide autostart entries are disabled by creating an identically-named .desktop file in $XDG_CONFIG_HOME/autostart and setting the Hidden=true key. That's what the autostart editor does when you disable an entry that lives in a user-read-only location. That's perfectly sufficient for normal use; if you have corner-case requirements, I suggest you drop to a shell and edit/rm the file manually. (Note that editing/removing system files can confuse package managers. I'd rather not encourage users to do that, especially when the current solution is perfectly reasonable.)