From a conversation with Tim Cross (for context, see the thread "Change
`customize-save-variable' to work under 'emacs -Q'?" on emacs-devel on
2011-07-12).

 > The core issue I see is that -Q is useful mainly because it
 > establishes a standard default environment.
[...]
 > Once we allow local customizations to be applied in this
 > environment, this standard base default environment no longer
 > exists. This may be fine, provided there is some mechanism that
 > makes what has been changed explicit and easy to reproduce.

I think that Customize already provides some function for listing
variables that are not at their default values, both Customized and
"rogue" values.  Its output could be added to the bug-reporter's buffer
(maybe it's already there in Emacs, but XEmacs doesn't do that yet). 
Perhaps it should be glossed with a comment that only defcustoms can be
listed this way.