Earlier quoted context omitted.
Actually, we have trained the model to convert to markdown and do semantic tagging at the same time. Eg, the equations will be extracted as LaTeX equations, and images (plots, figures, and so on) will be described within the ` ` tags. Same with ` `, ` `, . Also, we extract the tables as HTML tables instead of markdown for complex tables.
Have you considered XML. TEI, for example, is very robust and mature for marking up documents.
The fact that someone would go to all the work to build a model to extract the structure of documents, then choose an output format strictly less expressive than XML, speaks poorly of the state of cross-generational knowledge sharing within the industry.