People keep reinventing LaTeX, but poorly. Most of the issues described have already been solved by it at least 20 years ago, especially the semantics part. The tooling is mature, well understood and supported on all operating systems.
Haven't heard about archforms in a while ;) but it's not a technique for custom syntax, and since markdown is specified as a Wiki syntax with canonical mapping to HTML, there's no need for the kind of simplistic element and token renaming possible with archforms.
For example added an <nbsp> attribute to turn all spaces into non-breaking spaces, and used archforms to remove the attribute afterwards.
But yeah, maybe for Makrdown you don't need archforms. On the other hand, perhaps there is some super clever way to use archforms to get your reference links working.