I don't think anyone ever really expected to see widespread use of regexes to alter the
structure of a Markdown document. Honestly, while something like "look for numbers and surround them with double-asterisks to put them in boldface" is feasible enough (and might even work!), I can't imagine that a lot of people would do that sort of thing very often (or want to) anyway.
If a document is supposed to have structure - even something as simple as nested lists of paragraphs - it doesn't seem realistic to expect regular text manipulation tools to do a whole lot with them. Something like "remove the second paragraph of the third entry in the fourth bullet-point list" is well beyond any sane use of any regex dialect that might be powerful enough. (Keeping in mind that traditional regexes can't balance brackets; presumably they can't properly track indentation levels either.)
See also: TOML - generally quite human-editable, but still very much structured with potentially arbitrary nesting.