> [Markdown] struggles with things like embedded content and non-standard layouts.
I don't share that experience. I typeset all these documents using Markdown with pandoc's div extension, transformed into XHTML, and then passed to ConTeXt:
From XHTML, the document is transformed into TeX statements, which opens a world of possibilities. In the following video, custom styling is applied to nested contents:
Alternatives for authoring PDFs include LaTeX or similar markup languages, or GUI-based tools.
For many works, Markdown is more than sufficient for producing book-length texts (I've done this numerous times myself, either authoring my own works or transcribing/modifying books for improved access/readability). Markdown's benefit is that it is extraordinarily lightweight, and removes overhead from the authoring process.
Even where one ultimately chooses to migrate from Markdown to some more capable authoring format, Markdown remains useful for creating the original rough form of the work. Complex elements (figures, formulae, tables, etc.) can be indicated and, after document conversion from, say Markdown to LaTeX, fleshed out in full.
With tools such as Pandoc (see my earlier comments on it), it's trivially possible to create multiple outputs (I usually refer to these as "endpoints") of a document. I've used Makefiles to drive this process, such that I write source in Markdown and generate partial or full HTML documents,[1] other LWMLs,[2] PDF, ePub, straight ASCII/UTF-8/Unicode text, word-processing formats, etc., as I want. The set of Markdown + Pandoc makes this trivial in ways that, say, LaTeX alone isn't entirely suited.[3]
It's of course possible to use another LWML as the source format. Markdown has its limitations, but is most widely known and implemented, and limitations workarounds are typically reasonable.
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Notes:
1. A partial HTML doc may be useful for dropping into a larger document, and doesn't require global HTML elements such as the <html>, <head>, <body> tags, or others such as <nav> or <aside> in most cases.
2. Lightweight markup languages such as bbCode, AsciiDoc, RST, MediaWiki, OrgMode, etc., etc., see: <https://en.wikipedia.org/wiki/Lightweight_markup_language>. Useful when inserting the document into systems based on these formats.
"Markdown-formatted document should be publishable as-is, as plain text, without looking like it’s been marked up with tags or formatting instructions."
Any text editor (Notepad, TextPad, (neo)vi(m), Emacs, TextMate, Apostrophe, GhostWriter, Typora, etc.) will do. Markdown-specific editors have either a real-time preview or the ability to edit as WYSIWYM: