Lemons vs limes. They're both markup languages, but they have different purposes.

Yeah, using markdown to write a book is very limiting and doesn't offer the control needed for typesetting.

OTOH, using markdown to write is liberating - you only get a few markup options, so you can focus on the content:

    [It is] notable that the Feynman lectures (3 volumes) write about all of
    physics in 1800 pages, using only 2 levels of hierarchical headings: 
    chapters and A-level heads in the text. It also uses the methodology of 
    sentences which then cumulate sequentially into paragraphs, rather than the
    grunts of bullet points. Undergraduate Caltech physics is very complicated 
    material, but it didn’t require an elaborate hierarchy to organize.
    
    Edward Tufte, forum post, ‘Book design: advice and examples’ thread