Initialize config defaults independent of CLI usage

[about-code]

This should not be a breaking change.

The tool is advertised as a command-line tool not as a library package, so API usage is neither advertised nor recommended by any docs. But some API was exported, technically, mostly to integrate with other tools.

Potential users of run(conf) API function were more likely to run into errors when not providing config options which would have been initialized when using the CLI. API users which faced those errors are likely to have adapted by providing necessary values as part of a user configuration. With this change the API behaves like the CLI and initializes default values the same way as the CLI but user configuration values continue to win. So users who have already adapted to the old situation should not see any differences while new users could now pass the same minimal configuration to run(conf) as they could via CLI.