Click let's you build really nice command line libraries, but those are rigid and their structure is hard coded. A good example of what you wouldn't do with Click is logging configuration. You have a bunch of appenders, formatters and loggers and this is just not good with something like Click.

Hydra actually comes with built in Python logging configuration, it's just a part of the configuration object and Hydra is setting it up for the app: https://cli.dev/docs/tutorial/logging

You can override this from the command line (unlikely but could be useful), or completely replace it with your own logging config: https://cli.dev/docs/configure_hydra/logging

This kind of flexibility is a core part of how Hydra build the config, it's not limited to it's internal config (like logging) but extends naturally to the user config as well.