I don't think there's an easy way, but you can change or add system-wide config files. Most of the settings are provided by the ubuntu-mate-default-settings package. You can see a list of files included in this package.
Looks like the most important single file is /usr/share/glib-2.0/schemas/30_ubuntu-mate.gschema.override where most of the gsettings setting are made. Instead of editing that file — since it will get replaced if that package is updated or reinstalled — I think you can make a new file of the same type in that directory. If you start the filename with a higher number, like 35 or 40, it will be read afterwards so it will override the other ones.