Comment #4 on Launchpad #1864218 explains why everything is disabled. Looks like the Compiz folks want configuration files to be provided by the upstream projects:
So @Wimpy would need to bundle mate.ini into a package. Interestingly, he hadn't responded to the review 
I had a stab at fixing that - no luck. Will have another look at that again - it bothers me too!
Edit: Theme fixed.