There are several problems with the *embed-preview.html:

• Plots are not shown, only alt text (because plot links to notebooks/200-code.embed_files/figure-html/fig-200-pxrd-diffractograms-output-1.png but the image actually lives at notebooks/200-code_files/figure-html/fig-200-pxrd-diffractograms-1.png, the directory 200-code.embed_files does not exist).
• page-layout: full is not obeyed, meaning the body is quite narrow which looks awful especially code chunks
• Author names, affiliations and date are repeated at the top of the body text
• First code chunk is empty (first actual chunk is number 2)

For reference, this was the case with the following manuscript stanza in YAML:

manuscript:
  article: index.qmd
  meca-bundle: false
  notebooks:
    - notebook: index.qmd
      title: Manuscript notebook
    - notebook: notebooks/200-code.qmd

Render button in RStudio Server

Render button in RStudio executes quarto preview index.qmd --to html --no-watch-inputs --no-browse and causes notebook sidebar to link to notebooks/200-code-preview.html, which does obey my format.html.page-layout: full, but figure captions lack numbers and so cross-refs are broken.

Keyboard shortcut in RStudio Server

Ctrl+Shift+b in RStudio executes quarto preview --render all --no-watch-inputs --no-browse and causes notebook sidebar to link to notebooks/200-code.embed-preview.html.

quarto render in CLI

quarto render (executed from CLI) causes notebook sidebar to link to notebooks/200-code.embed-preview.html (but not every time?).

quarto preview in CLI

quarto preview --render html --port 25598 --host 0.0.0.0 --no-browser (in the CLI) causes sidebar to link to notebooks/200-code.embed-preview.html.

Depends on YAML in a non-obvious way

But after commenting out the entire manuscript.notebooks list, the situation changes!
Now none of the above methods link to to the *embed-preview.html version - in fact, no such file is even rendered (only the *-preview.html is rendered).

• https://quarto.org/docs/manuscripts
• https://github.com/quarto-dev/quarto-cli/issues/11475
• https://github.com/quarto-dev/quarto-cli/discussions/6180