The Windows registry is a database. Introduced in Windows 3.1 to handle COM classes, and later extended as the preferred config mechanism over .ini files.

If you are a Windows user you'll notice the problems that it introduces in terms of security and maintainance. Files are much better in both aspects.

To me the underlying issue is not centralization into a single database, but the usability of advanced configuration. Every OS have multiple attempts to resolve that problem, which ended in more fragmentation for end users (i.e. macOS plist / registry / rc files / etc).

a filesystem is a database