Unity 3D uses GConf, but Unity 2D uses DConf. Why is that and is there an overview of where the different parts of Unity (scopes, lenses, etc) are stored in which configuration system?
GConf if being replaced by DConf. New applications should use the latter. However, Unity 3D is based on Compiz, which itself still uses GConf. So Unity 3D inherits from that. Unity 2D is new, so it uses DConf.
The parts of Unity that isn't shown, such as data providers, scopes and lenses, are stored in DConf.