.github directories within individual repositories are used to house things like templates, READMEs, Codes of Conduct, etc that are specific to the individual repository.
Similarly, a .github repository is a special repository designed to mimic the behavior of its sister directories, but at an organizational level. Meaning, if something like a Pull Request template is not defined in the individual repository's .github directory,
Pull Requests, when opened, will default to using the PR template defined in the organization-level .github repository. Defaults from this .github repository can be overriden by explicitly configuring the equivalent directory in any given code repository.