This is not a bug, but rather misconfiguration..
If you start Xgl as a session (rather than having GDM hosted on Xgl), X cookies 
are not forwarded by default. Make sure your Xgl starter script contains two 
lines like:
cookie="$(xauth -i nextract - :0 | cut -d ' ' -f 9)"
xauth -i add :1 . "$cookie"


and you will get full logout options.

** Changed in: xserver-xgl (Ubuntu)
       Status: Needs Info => Rejected

** Changed in: gnome-session (Ubuntu)
       Status: Needs Info => Rejected

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Incomplete logout options with XGL
https://bugs.launchpad.net/bugs/36321
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