They used to support IPv6. When they added HTTPS support they removed it because of it [1]. Which is a complete nonsense reason. Using the old IPv6 range works for *.github.io domains even now.
But IIRC, you can fetch GitHub Pages custom domains over IPv6 with HTTPS too, but you don't get the correct certificates, because they simply don't have an IPv6 range pointing to the newer HTTPS-supporting infra.
[1]: https://github.com/isaacs/github/issues/354#issuecomment-385...