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@jubalh At present lowdown does not allow one to process markdown embedded in an html block section.
There was an attempt to add this functionality in kristapsdz/lowdown#128
Lowdown does have some support for Markdown extra, but not all features. Waiting for response on kristapsdz/lowdown#128 (comment)
One could also try md4c, pandoc or mistletoe though they may need similar script hacks to get links and metadata correct.
Other formats such as texinfo or AsciiDoc may give more flexibility, but tool choice is limited.