With apologies, I do not have any LaTeX domain knowledge, therefore this issue will be a conversation between various instances of Claude.

TL;DR: there are paths forward, but the current recommendation is to use footnotes and not margin notes in order to produce accessible PDFs using LaTeX.

Errors:

• StructTreeRoot shall not contain <P>/<Caption>/<Figure>/<Table>/<Div>/<Part>
• The structure tree root shall contain a single Document structure element
• <P> shall not contain <Aside>/<Part>/<P>

Cause: All these tests use margin layout (.column-margin or column: margin).
Quarto's filters generate:

• \marginnote{\begin{footnotesize}...\end{footnotesize}} for text
  (src/resources/filters/layout/latex.lua:215-238)
• \begin{marginfigure}...\end{marginfigure} for figures
  (src/resources/filters/layout/latex.lua:554)
• \begin{margintable}...\end{margintable} for tables
  (src/resources/filters/layout/latex.lua:643-663)

These come from the sidenotes and marginnote LaTeX packages (injected at
src/resources/filters/layout/meta.lua:106-116). These packages predate PDF
tagging and don't cooperate with tagpdf:

• \marginnote creates content in a separate output stream that escapes the
  Document structure element entirely, placing children at StructTreeRoot.
• tagpdf assigns an <Aside> role to margin content but nests it inside an
  active <P> context, which is invalid per PDF/UA-2.
• The result is structure elements (<P>, <Caption>, <Figure>, etc.) appearing
  directly under StructTreeRoot instead of inside <Document>.

Files:

File	Margin content
2024/05/06/9582.qmd	Multiple .column-margin divs with figures and text
2024/06/24/10112.qmd	R table with column: margin
typst/margin-layout/margin-figure-crossref-interleaved.qmd	Figures with .column-margin class
article-layout/tables/compute-table-margin.qmd	R table with column: margin
2022/09/30/caption-footnotes/test.qmd	Also affected (uses figure captions; see section 3)

Problem in: LaTeX packages (sidenotes/marginnote). These packages are not
tag-aware. Fixing this requires either:

• Upstream patches to sidenotes/marginnote for tagpdf compatibility
• A different LaTeX approach for margin content when tagging is enabled
• Skipping UA-2 validation for margin-layout tests until the ecosystem catches up