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Handwritten HTML with limited tags works just as well for many purposes (just forbid div, span, and a few others and the complexity you see in most webpages evaporates). The important part is using a text-based format from which information can be extracted even if the fancier display protocols become obsolete.
Not really. HTML has a formal standard and definition that covers how to properly handle most corner cases that can arise when displaying it. Markdown has no overarching formal standard and exists in multiple dialects which are not always compatible with each other.
On the gripping hand, HTML involves more keystrokes (and technically speaking you need to include a bit of boilerplate in the file for it to be proper HTML). So it depends on whether you’re willing to do a bit more typing to make sure that no one can possibly confuse your italics with boldface.