My gut reaction is that it sounds like a terrible idea. Markdown is designed at the outset as a markup language, meant to imbue formatting and structure to human-readable text. But it lacks a formal grammar or a strictly defined mapping from syntax to parse tree, so different tools may interpret the same document differently (i.e. there are many Markdown “dialects”). Markdown has no inherent support for any kind of data types other than text; it has lists, but nothing that would obviously be “map” or key-value data structures.

Indeed, if you’re going to make use of Markdown to store structured data like a config file, I wager the result will start looking a lot like YAML. At which point - why not just use YAML directly?