To repro:

1. Run latest master of Jetpack.
2. With Markdown module off, enable it.
3. Add a new post/page, enter some markdown.
4. Publish it.

What I expected: markdown to be changed to HTML.

What happened: markdown comes out raw. Screenshot:

I think this is because the new setting under Settings > Writing does not automatically get turned on:

Probably related to #6406 cc @eliorivero