Sorry, no info concerning ConTeXT.
You don't have to use proprietary tools. An easy way to create ebooks from Markdown files (or other sources) is Pandoc. https://pandoc.org/
I produce all of my ebooks in this way. In most cases they validate without errors. If there are some errors though I use Calibre to fix them manually. Thanks, I didn't think of Pandoc, I'll give it a try. In the past, I have tried to create some simple content (slides) with Markdown, but my conclusion was that if you know TeX, it doesn't make sense to use Markdown :)
Perhaps this is a silly question (excuse my ignorance about the topic): what if you want to add some stylistic touches to your ebooks, such as initials? Or Non-breaking spaces? How about adding, say, a text box with a different background and a smaller font?
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Or fine control page numbering, headers, footnotes, ligatures, or the spacing between paragraphs, or center a separator as above? Do you need to modify the generated CSS for that, or would ConTeXt (or Pandoc) allow you to take care of (some of) those things?
Nicola
For Pandoc: Some things can be tweaked with pandoc, but for anything that is a bit more advanced you'll probably need a custom CSS. For special content you can use spans and divs. In your custom CSS you can define how those elements should be rendered. Sounds pretty similar to what Hans wrote in his response. Probably the main questions are if you prefer to work with pandoc markdown or with ConTeXt sources, and if you need additional output formats. Denis