Markdown works really well with calibre and plain text sources.
See
https://daringfireball.net/projects/markdown/ then use calibre's options on the "TXT Input" section of the conversion dialogue.
Pre-processing your plain text with some regex can be an efficient way of introducing Markdown for calibre to detect so that your book gets some structure and style.
If you want to extend Markdown's styling then you can add your own syntax in your plain text file and then post-process the converted book with calibre's editor and regex.
I'm not sure if you can change the options with ebook-convert but you could set them as defaults.
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@porphyry5 : Do you really still have a working PRS-300 ?