In addition to what squale said (it sure would be great if beta-testers could modify options without having to recompile or design a GUI for that purpose!):
* it easily ensures backwards compatibility as new features are introduced; it allows common configuration parameters to be shared across several programs
* if you impose the order in which you parse, yes; but conflib allows sections and definitions to be moved around within the file, just as it allows you to keep unchanged keys that you can't handle (think of this config file :

[DefaultApplications]
TextViewer = "AMSTextEdit"
TextEditor = "AMSTextEdit"

- your favourite text viewer could modify the default text viewer, even though it doesn't even know about the TextEditor key! thus it also provides some form of forward compatibility)