> one of their goals was to get Github and StackExchange 'out of the markdown business' but neither use CommonMark

FWIW, StackExchange [uses CommonMark][1] for their new StackOverflow Documentation site and has [been planning][2] to migrate Q&A to CommonMark for some time now.

[1]: https://meta.stackexchange.com/questions/125148/implement-st...

[2]: https://meta.stackexchange.com/q/238957/192171