QuartoMarkdownBase64 works with cross references but not citation keys in LaTeX/PDF

Bug description

This is related to https://github.com/quarto-dev/quarto-cli/issues/3340 and including citation keys in tables (manual ones and ones made with things like {gt})

{gt} recently added fmt_markdown(), which injects <span data-qmd="blah"></span> stuff around citations and cross references in HTML output, so that Quarto correctly processes the citations and cross references.

In https://github.com/quarto-dev/quarto-cli/pull/7451, Quarto added a similar feature for LaTeX output, adding a \QuartoMarkdownBase64{} command for processing/protecting citations and cross references.

\QuartoMarkdownBase64{} works for cross references, but not for citations.

Steps to reproduce

With this document:

---
title: "Citations in tables"
format: 
  html: default
  pdf: 
    keep-tex: true

references:
- type: article-journal
  id: Lovelace1842
  author:
  - family: Lovelace
    given: Augusta Ada
  issued:
    date-parts:
    - - 1842
  title: >-
    Sketch of the analytical engine invented by Charles Babbage, by LF Menabrea, 
    officer of the military engineers, with notes upon the memoir by the translator
  title-short: Molecular structure of nucleic acids
  container-title: Taylor’s Scientific Memoirs
  volume: 3
  page: 666-731
  language: en-GB
---

$$
a^2 + b^2 = c^2
$${#eq-math}

```{r}
library(gt)
tibble::tribble(
  ~Thing, ~Citation,
  1234, "@Lovelace1842",
  5678, "@eq-math"
) |>
  gt() |> 
  fmt_markdown(Citation)
```

…when rendered to HTML, everything works great thanks to @rich-iannone's updates to fmt_markdown():

 

When rendered to PDF, though, neither of the citation keys are processed (likely because {gt} doesn't do anything with \QuartoMarkdownBase64{} yet?):

 

So I tried making the table manually with LaTeX:

```{=latex}
% QExvdmVsYWNlMTg0Mg==} is "@Lovelace1842" in base-64 encoding
% QGVxLW1hdGg= is "@eq-math" in base-64 encoding
\begin{tabular}{cc}
Thing & Citation \\
1234 & \QuartoMarkdownBase64{QExvdmVsYWNlMTg0Mg==} \\
5678 & \QuartoMarkdownBase64{QGVxLW1hdGg=} \\
\end{tabular}
```

Quarto emits this LaTeX:

% QExvdmVsYWNlMTg0Mg==} is "@Lovelace1842" in base-64 encoding
% QGVxLW1hdGg= is "@eq-math" in base-64 encoding
\begin{tabular}{cc}
Thing & Citation \\
1234 & @Lovelace1842 \\
5678 & Equation~\ref{eq-math} \\
\end{tabular}

…and this PDF:

 

The @Lovelace1842 citation key is unprocessed, while the @eq-math cross reference is converted to the correct LaTeX.

Expected behavior

I was hoping that the @Lovelace1842 citation key in the table would get converted to a bibliographic reference and be processed by citeproc, but it looks like citation processing is happening at a different stage in the Quarto pipeline?

Actual behavior

The @Lovelace1842 citation key is unprocessed, while the @eq-math cross reference is converted to the correct LaTeX.

Your environment

• IDE: RStudio 2024.04.0-daily+581
• OS: macOS Sonoma 14.4.1

Quarto check output

Quarto 1.5.27
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.11: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.41.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.5.27
      Path: /Applications/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: (external install)
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/andrew/Library/TinyTeX/bin/universal-darwin
      Version: 2023

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.11.5
      Path: /opt/homebrew/opt/python@3.11/bin/python3.11
      Jupyter: 5.3.0
      Kernels: python3

[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........OK
      Version: 4.3.2
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
      knitr: 1.45
      rmarkdown: 2.25

[✓] Checking Knitr engine render......OK

❯ quarto check > ~/Desktop/bloop.txt
Quarto 1.5.27
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.11: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.41.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.5.27
      Path: /Applications/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: (external install)
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/andrew/Library/TinyTeX/bin/universal-darwin
      Version: 2023

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.11.5
      Path: /opt/homebrew/opt/python@3.11/bin/python3.11
      Jupyter: 5.3.0
      Kernels: python3

[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........OK
      Version: 4.3.2
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
      knitr: 1.45
      rmarkdown: 2.25

[✓] Checking Knitr engine render......OK