not sure to understand your questions now, gconf has system defaults and you 
can system admin values and user configuration, if you do change those go to 
the user configuration which is not remove when the package is uninstalled 
because those are your datas and it's not up to the system to decide whether to 
remove those or not
now when uninstallion a software the corresponding ubuntu system keys are 
unregistred, so if those are still listed that's either user configuration or a 
bug in the software

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gconf-editor shows entries/folders that do not exist anymore
https://bugs.launchpad.net/bugs/217750
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