There is the longform plugin:
Not tried it myself, but it seems like a really nice way to stitch together docs.
Unfortunately, it does not seem to do embeds.
I’m sad to say that of the two manuscripts I’ve started trying to put together in directly in obsidian, in both cases I gave up and just wrote it out in a LaTeX document from scratch.
One challenge I’ve faced when trying to move from vault to final manuscript is the handling of internal links. I think pandoc ships with a filter that strips the link markup from mediawiki style links, but that then leaves the [[ugly-and-probably-meaningless]] file paths in the text. I’ve forced myself to alias every internal link with a phrase that works even if the link is stripped away to support this outflow approach. (Paradoxically, my attempt at making my information more robust made it especially vulnerable/fragile to the 1.2.2 pipe bug wreaked – so much havoc with my vault! 
)
But that solves only part of the outflow challenge. The other one is citations. My vault notes maintain references to source notes (e.g., [[@darwin1856-origin]]), but pandoc needs actual citations. Fortunately, the file naming convention the Citations plugin suggests works really well when stripping the external [[ ]] brackets … BUT then the wikilink processor breaks this. I finally hacked in a mostly-working Pandoc filter that preserved the source references as pandoc citations.
The other issue was that eventually I felt I needed more control over layout, math expressions, and (especially) image embedding, layout, sizing etc. than any pure Markdown format flow could give me.
Really interested in seeing/hearing about other folk’s workflows that might work better .