### Bug description

Hej!

In a larger project, I would like to use my own `latexmk` pipeline because manually running `latexmk` with the LaTeX file generated by Quarto works successfully whereas compilation is unsuccessful when I try to generate the PDF with quarto and `pdf-engine: latexmk`. Based on the docs, I assumed I could opt out of Quarto's machinery by setting `latex-auto-mk: false`. However, changing this setting does seem to make a difference (as someone else had noticed before apparently: https://github.com/quarto-dev/quarto-cli/discussions/819#discussioncomment-2704475). In contrast to other configurations, these options also don't show up in the pandoc/metadata output in the terminal.

So I tried to set some of the other `latex-...` options and they also did not seem to affect compilation. For instance, I played around with the following somewhat minimal example:
```md
---
title: MWE
format:
  pdf:
    pdf-engine: latexmk
    pdf-engine-opt: '-verbose'
    latex-auto-mk: false
    latex-output-dir: "/home/david/quarto-mwe/"
---

A MWE for debugging the `latex-` options.
```
I rendered it by running
```shell
quarto render mwe.qmd --log-level=debug
```
in the terminal. Both with Quarto 1.2.335 and 1.3.34 (Fedora 37), the `latex-...` options do not change the output in the terminal and, e.g., regardless of the option `latex-output-dir` always a directory `/tmp/...` is used by latexmk.

Am I doing something wrong or do these options not work currently?

### Checklist

- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.
2023-03-09T14:52:49Z
devmotion
closed
`latex-...` options not picked up?
https://github.com/quarto-dev/quarto-cli/issues/4733