I would argue against using markdown simply because it’s not at all a tool for the job and one must avoid the pitfall of being tempted to see very problem as solvable by the same tool just because it is the sole tool available.
Markdown shines as a simple (poorly standardize) format that allows to express basic formatting in text fashion. It comes very short when it comes to standardisation, expressivity (even for text), structure (even for tables) and was simply never designed for anything like connectivity, graphs, being parsed unambiguously, or anything else than simple formatted text.
What’s the added value of using markdown versus just another better human readable but specialized language? The page is not mean’t to be editted in the editor anyway. Pushing ackward concepts into markdown will just lead to supporting exotic and hard to parse syntax anyway, i have no doubt it is doable and perhaps language must be expanded, but selecting the right tool for the job seems to me more important than making a text styling language suddenly expanding into representing highly structured data