We run the audit as the first step of nearly every SEO engagement, and we run it as a standalone paid project for businesses who want the diagnosis without the retainer. Either way you keep it, including the parts that recommend work we would not be doing.
The reason it is worth paying for rather than taking a free automated report is that the automation is the easy part. Any tool can tell you that forty pages have missing meta descriptions. Knowing whether that matters for your site, and what to do about the three things that actually do matter, is judgement.