Microsoft had multiple Github Enterprise accounts before the acquisition, owned by multiple teams independently inside of Microsoft. They chose to use these instead of Microsoft's own internal repository (some VSS-based thing I think), which management ordered them to use.

More internal Microsoft code was being hosted by Github instead by Microsoft.

However, the Microsoft account on Github seems to only be public repositories, or repositories being prepped to be public. Actual internal stuff is hosted by one or more Github Enterprise accounts, the alleged hack does not claim they were hacked as well.