For me, a key tenant of any good note taking system is low friction. Leaning on an LLM feels like significant friction. Formatting something into HTML manually also feels like a lot of fiction. Individual HTML files for notes would also be a friction filled experience for opening and browsing, without some kind of template to allow for navigation of the notes within the browser. This ends up turning into a local wiki very quickly.

I was about to comment: "HTML creates too much friction after doing all sorts of visual explainers" ... thanks for articulating it well.

As a layer of abstraction, it also creates more requirements: need a browser, likely need includes/cdn libs to avoid bloat, all sorts of other things. Markdown is consumable, diffable, shareable in raw form - and you can add enrichment layers on top without much effort.