They could have avoided the bulk of these problems by the following:

5. License Grant to Other Users

If your project doesn't have a license attached, then the rights you provide GitHub and users are as follows:

You agree to allow others to view and "fork" your repositories (this means that others may make their own copies of your Content in repositories they control).

If you set your pages and repositories to be viewed publicly, you grant each User of GitHub a nonexclusive, worldwide license to access your Content through the GitHub Service, and to use, display and perform your Content, and to reproduce your Content.

Choosing a License for the repo supersedes the above rights declaration and reverts completely to the License of your choice.

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There's cases where I'm using someone else's GPL3 code. Im using it because of the GPL and am granted rights. I can't comply with the "rights" GH wants because I don't have them to give.

I also have projects that I'd like to share as GPL, but not as BSD or MIT. My choice. The existing version grants GH an effective BSD license for everything on there.