Then it seems like the issue you have is how vendors are storing keys in the registry, not the registry itself. In your example, if nginx made a single node in the registry with all its keys under that then it would be just as easy to remove that single node as it would be to remove the single directory.

However in the real world it is never as simple as you suggest. Linux apps often litter the filesystem with data. an app might have files in /etc and /opt with shortcut scripts in /root/bin and /usr/sbin. Config files in /home and /usr directories. Linux file systems are just as littered as windows registries in my experience, if not worse because they differ in different distros.