Adding label to callout in filter fails to generate correct xref

Bug description

When writing a filter for callouts, but not sections - Quarto does not correctly detect xref label that I have added in the filter.

See: https://github.com/matthew-brett/filter-notes-no-xrefs

In this repository, I am trying, through filtering, to generate the equivalent output as I would get from the following direct.qmd input (also in the repository:

---
title: Direct version of page with note
---

## My direct header {#sec-my-direct-section}

See @sec-my-direct-section

::: {#nte-my-direct-note .callout-note}
## My direct heading
:::

See @nte-my-direct-note.

I am manipulating the following input .qmd document using a couple of trivial (in my case) Panflute Pandoc JSON filters:

---
title: Filtered version of page with note
---

## My header mark-for-section-target

See @sec-my-filtered-section

::: {.callout-note}
## My filtered heading
:::

See @nte-my-filtered-note.

My filters replace the AST for ## My header mark-for-section-target with ## My filtered header {#sec-my-filtered-section} - and this works correctly to generate the section xref target. But my filters also replace the AST for the callout note with:

::: {#nte-my-filtered-note .callout-note}
## My filtered heading
:::

and this fails - both in generating correct HTML output for the callout note, and in generating the xref for the callout note. See below for the steps to reproduce, and more detail.

Steps to reproduce

See: https://github.com/matthew-brett/filter-notes-no-xrefs.

I believe my filters are correct, and I have explicitly specified these filters should run before quarto, although I believe this is the default. The filters are add_section_target.py and add_callout_target.py in the repository.

To reproduce, clone the repository. quarto render direct.qmd generates the expected HTML output without warnings. quarto render filtered.qmd gives the warning WARNING (/Users/mb312/dev_trees/quarto-cli/src/resources/filters/./crossref/refs.lua:127) Unable to resolve crossref @nte-my-filtered-note showing that the callout note filter output was not interpreted correctly, confirmed by the output HTML. quarto render direct.qmd --to markdown generates this (as expected):

---
title: Direct version of page with note
toc-title: Table of contents
---

## My direct header {#sec-my-direct-section}

See [Section 1](#sec-my-direct-section){.quarto-xref}

::: {#nte-my-direct-note}
> **Note 1: My direct heading**
:::

See [Note 1](#nte-my-direct-note){.quarto-xref}.

However, quarto render filtered.qmd --to markdown generates this:

---
title: Filtered version of page with note
toc-title: Table of contents
---

## My filtered header {#sec-my-filtered-section}

See [Section 1](#sec-my-filtered-section){.quarto-xref}

<div>

> **My filtered heading**

</div>

See **?@nte-my-filtered-note**.

Expected behavior

See above. The filtered output should be equivalent to the following direct output, and adding the xref to the Markdown, via the filter, should generate the xref target, as for the direct version.

Actual behavior

See above.

Your environment

• IDE - command line
• OS - macOS Sequoia 15.1

Quarto check output

Quarto 99.9.9
[✓] Checking environment information...
      Quarto cache location: /Users/mb312/Library/Caches/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.4.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.46.3: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 99.9.9
      commit: adc7186f0ee20ed125588cd603330beb2e76bc71
      Path: /Users/mb312/dev_trees/quarto-cli/package/dist/bin

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

[✓] Checking LaTeX....................OK
      Using: Installation From Path
      Path: /Library/TeX/texbin
      Version: 2024

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

[✓] Checking Python 3 installation....OK
      Version: 3.10.14
      Path: /Users/mb312/.virtualenvs/resampling-with/bin/python3
      Jupyter: 5.3.0
      Kernels: python3, ir, xibabel, exercises

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

[✓] Checking R installation...........OK
      Version: 4.4.1
      Path: /opt/homebrew/Cellar/r/4.4.1/lib/R
      LibPaths:
        - /Users/mb312/Library/R/arm64/4.4/library
        - /opt/homebrew/lib/R/4.4/site-library
        - /opt/homebrew/Cellar/r/4.4.1/lib/R/library
      knitr: 1.47
      rmarkdown: 2.28

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