I think you found a very good prompt/technique to extract mostly the high level stuff without making the diagrams too complicated. And then elk.js seems to do the layout.
Deepwiki.com also has some usable autogenerated architecture diagrams worth a look.
OKF seems OK, but bound to Markdown.
A Markdown document can be turned into an OKF document by adding a 'type' to the frontmatter YAML.
What about a knowledge graph language, which can be stated in Markdown prose, in Markdown code blocks, but also everywhere a text field is waiting for you?
In the minimalistic language https://ddot.it you can link outside the Markdown world, to files, URLs or even just labels.
Like OKF it's just a format.