MateConf is a system that was invented to make application preferences more manageable for system administrators.
MateConf stores data in the user space in $HOME/.mateconf:
mateconftool-2 is the MATE configuration tool. It is meant to be used from command line
$ mateconftool-2 -R /desktop/mate
That will display some of the MATE desktop settings.
The MateConf Editor is a graphical application and as such is more targeted towards the general user.