You shouldn’t use Markdown for content anymore

Authors are supposed to submit a manuscript with the least amount of formatting. Images are given in a separate folder and only referenced in the manuscript, maybe with a couple notes on alignment. Markdown precisely forces the author to follow this contract. Just write the content and organize the chapters.

Ultimately it's the publishing house's job to format and create the final rendition, insert and design the fancy tables that you see in, for example, a chemistry textbook. In the corporate world, their publishing houses are called technical writers/content strategy/learning development/marketing departments.

So the idea of not using Markdown is both right and wrong. It's totally unfair to expect contributors and authors to understand everything about formatting and publishing. But, Markdown is only the first step in an entire toolchain. If people cannot tell what part of the process they fall on (authoring vs publishing) then it's going to be confusing.