Also, we extract the tables as HTML tables instead of markdown for complex tables.
(I'm a MyST contributor)
As a project, the tooling to parse MyST Markdown was built on top of Sphinx, which primarily expects ReST as input. Now, I would not be surprised if most _new_ Sphinx users are using MyST Markdown (but I have no data there!)
Subsequently, the Jupyter Book project that built those tools has pivoted to building a new document engine that's better focused on the use-cases of our audience and leaning into modern tooling.
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.
If goal is to parse this output programmatically, then I agree a more structured markup language is better choice.
Have you considered using something like Pandoc’s method of marking them up? Footnotes are a fairly common part of scanned pages, and markdown that doesn’t indicate that a footnote is a footnote can be fairly incomprehensible.