Based on "application's files all over the hierarchy" it seems you talk about configuration files (data files can be spread all over, in any operating system; binaries in Linux reside in a few directories (/opt and /usr)).
If you refer to gconf/dconf, AFAIK they require a specialized tool but they're not scattered (you interact through the tool, after all, so they're centralized).
Possibly you refer to the Freedesktop configuration files. Those are definitely scattered, and some concepts are very obscure (the defaults system is indeed terrible, as it's scattered, and it has different concepts of default). However, they don't require specialized tools - in my experience, they're always text files.