Funny, I use the opposite approach. If I can't configure and manage something via the filesystem, I usually stay clear of it.
Specifically, not relying on the filesystem means I can't easily browse configuration, I can't have version control, and I can't use my configuration manager to have events trigger when things change.
No, i think raziel2p understands. If you're using a configuration management tool like Puppet or Ansible, by far the easiest way to manage a piece of software is through a configuration file on disk that the configuration management tool can manage directly: it's easy to see the current state, and to make changes. Anything that requires a tool or an API requires you to interpose some sort of update mechanism between the configuration management tool and the software, which doesn't have the transparency of a simple file.