This is way for us, the maintainers of the action, to quickly disable built-in queries without having to go through the process of changing the codeql bundle release. This can be used as a temporary measure while the code scanning suite is changed and the bundle updated, which could take a couple of weeks.

You can verify it's working by looking in the logs on the integration test runs (e.g. https://github.com/github/codeql-action/runs/772313587).
It prints out how many queries are run and you can see that there are two fewer C# queries compared to than a run against master (e.g. https://github.com/github/codeql-action/runs/772066021)

Merge / deployment checklist

• Run test builds as necessary. Can be on this repository or elsewhere as needed in order to test the change - please include links to tests in other repos!
  • CodeQL using init/analyze actions
  • 3rd party tool using upload action
• Confirm this change is backwards compatible with existing workflows.
• Confirm the readme has been updated if necessary.