Checks-out automatically enables GitHub protected branches for your repositories’ default branch. You can further customize or disable this behavior by navigating to your repository branch settings screen in GitHub.
GitHub Enterprise 2.4 does not have an API for protected branches. As a result you will need to manually configure protected branches after enabling your repository in checks-out. This can be done by navigating to your repository branch settings screen in GitHub Enterprise (pictured above).
Checks-out automatically enables itself for the default branch. If you would like to enable checks-out for additional branches you can manually configure additional branches in your repository branch settings screen in GitHub.
Checks-out automatically adds itself as a required status check. If you would like to enable additional status checks, such as continuous integration or code coverage, you can further customize this behavior in your repository branch settings screen in GitHub.