Figure numbering is broken in HTML output while using newest RStudio 2024.04.0 with pandoc 3.x

[N0rbert]

Below is the minimal reproducible example (index.Rmd file):

---
title: Figure cross-reference issue in HTML
documentclass: book
site: bookdown::bookdown_site
output:
    bookdown::html_document2: default
---

```{r eval=TRUE, include=TRUE}
sessionInfo('bookdown')
rmarkdown::pandoc_version()
xfun::session_info('bookdown')
```

# Zero 1 {-#zero1}

Some text in 1st unnumbered section.

# Practically long header about some theories {#theory}

## Markdown Syntax {#markdown-syntax}

...

### Images {#markdown-syntax-media}

First figure of first section is below, it reference is Fig. \@ref(fig:md-logo).

![(\#fig:md-logo) Markdown logo](https://upload.wikimedia.org/wikipedia/commons/thumb/4/48/Markdown-mark.svg/208px-Markdown-mark.svg.png)

...

While knitting this document using RStudio 2024.04.0 Build 735 with integrated latest pandoc 3.1.11 to HTML I get the wrong rendering

Here my figure is not numbered. So the cross-reference works as expected, but "Figure 1.1: " is not shown.

It is fresh installation of Ubuntu MATE 24.04 LTS.
Other details:

> xfun::session_info('bookdown')
## R version 4.3.3 (2024-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 24.04 LTS
## 
## Locale:
##   LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##   LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##   LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##   LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##   LC_ADDRESS=C               LC_TELEPHONE=C            
##   LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## Package version:
##   base64enc_0.1.3   bookdown_0.39.1   bslib_0.7.0       cachem_1.0.8     
##   cli_3.6.2         digest_0.6.35     evaluate_0.23     fastmap_1.1.1    
##   fontawesome_0.5.2 fs_1.6.4          glue_1.7.0        graphics_4.3.3   
##   grDevices_4.3.3   highr_0.10        htmltools_0.5.8.1 jquerylib_0.1.4  
##   jsonlite_1.8.8    knitr_1.46        lifecycle_1.0.4   memoise_2.0.1    
##   methods_4.3.3     mime_0.12         R6_2.5.1          rappdirs_0.3.3   
##   rlang_1.1.3       rmarkdown_2.26    sass_0.4.9        stats_4.3.3      
##   tinytex_0.50      tools_4.3.3       utils_4.3.3       xfun_0.43        
##   yaml_2.3.8

> rmarkdown::pandoc_version()
## [1] '3.1.11'

Running remotes::install_github("rstudio/bookdown") does not help.
Also please note that RStudio 2023.03.2-454 with pandoc 2.19.2 produces correct rendering.