I think the default config files used when creating a new user are in /etc/skel but I’m not sure how to setup a default theme, as it’s stored in Dconf.
EDIT: oh, I hadn’t looked at the link you put. I guess you’ll simply have to create an override file in /usr/share/glib-2.0/schemas with the Dconf settings you want to change. Look at ubuntu-mate.gschema.override to check the Dconf keys you need and create your own .override file with the values you want. You’ll have to name it so that it is loaded after the others. As they’re sorted alphabetically, I guess you’ll have to use a name “higher” than “ubuntu-mate.gschema.override”, you can try something like “zzz.override”.
The values you’need to change should be these ones:
[org.mate.interface]
icon-theme='Ambiant-MATE'
gtk-decoration-layout='menu:minimize,maximize,close'
gtk-theme='Ambiant-MATE'
font-name='Ubuntu 11'
document-font-name='Ubuntu 11'
monospace-font-name='Ubuntu Mono 13'
[org.mate.Marco.general]
center-new-windows=false
compositing-manager=true
side-by-side-tiling=true
theme='Ambiant-MATE'
titlebar-font='Ubuntu Medium 11'
org.mate.interface would be for the Gtk and icon themes, while org.mate.Marco.general would be for the Marco/Metacity (windows titlebar) theme. Of course, you don’t have to set all the values, keep only the keys you want to override.