Hi @transisto, before it is converted into a Markdown, the shortcode is rendered as HTML (Basically, it is processed with the WordPress logic) then converted into a Markdown.
As for the shortcode with no equivalent, they stay there as is as text in Markdown format. (Example: if there's no shortcode handler for "[wp_steem_debug]", it will display as text in Steem post "[wp_steem_debug".
PS: Thanks for supporting this. Greatly appreciate it! :)