> First, browsers would need to agree on which flavor of Markdown, what extensions, and so on.

The correct answer is CommonMark. At that point extensions don't matter, since there's a common enough base that a Markdown document written with unsupported extensions in mind will still look decent. Reference code is abundant and permissively licensed. There's no good reason to pick any other flavor (and most other flavors are compatible enough with CommonMark for it to be a non-issue anyway).