When using Compiz, it's hard to imagine working with "default" settings. Enabling / Disabling features and adjusting the plugins behaviors via ccsm is almost mandatory. Some other important settings, like OpenGL, number of desktops, etc are also inside ccsm.
But it doesn't seem like ccsm is being changed to adhere to the desktop defaults in anyway. And if compiz is mandatory for running the unity desktop, it may create confusion to have both a "settings" interface (mouse, shortcuts, background, etc) and also a compiz settings program.
Do you think they'll move ccsm settings to other interface? To the settings window maybe? In PP? PP+1?