"When a school or employer supplies your GitHub account, they assume the role of Data Controller for most Personal Data used in our Services. This enables them to: Manage and administer your GitHub account, including adjusting privacy settings. Access and utilize your Personal Data, which includes details on how you use the Services, as well as your content and files."
When using an organization-provided GitHub account, the organization gets broad access to your personal data, content, files, and usage details, and can adjust your privacy settings on your behalf.