Markup is "The code we [Github] use to render README.your_favorite_markup". They list Redcarpet as their library for Markdown. This, in turn, uses Sundown. Whether this is used for all of the site I'm not sure.
It also claims to have "massive extension support".
Sundown has optional support for several (unofficial) Markdown extensions, such as non-strict emphasis, fenced code blocks, tables, autolinks, strikethrough and more.
For full detail you'll probably have to dig into those libraries.
Bonus points if you can point me to a resource that shows how github flavored markdown and commonmark overlap and how they are different.
Sundown claims to be "fully standards compliant" with Markdown v1.0.0 and v1.0.3, but for the life of me I cannot find those versions. Only v1.0.1 and CommonMark which is at 0.26.
Sundown passes out of the box the official Markdown v1.0.0 and v1.0.3 test suites, and has been extensively tested with additional corner cases to make sure its output is as sane as possible at all times.
The Github Markdown extensions are documented in their Mastering Markdown guide.