`embed-resources` option doesn't work when rendering from non-input directory

Bug description

In quarto render in pre-release version 1.4.528, "--to " is incompatible with "dashboard". The output becomes funky if --to dashboard is used and these warning are outputted:
[WARNING] Could not fetch resource dashboard_files/libs/clipboard/clipboard.min.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-html/quarto.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-html/popper.min.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-html/tippy.umd.min.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-html/anchor.min.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-html/tippy.css [WARNING] Could not fetch resource dashboard_files/libs/quarto-html/quarto-syntax-highlighting.css [WARNING] Could not fetch resource dashboard_files/libs/bootstrap/bootstrap.min.js [WARNING] Could not fetch resource dashboard_files/libs/bootstrap/bootstrap-icons.css [WARNING] Could not fetch resource dashboard_files/libs/bootstrap/bootstrap.min.css [WARNING] Could not fetch resource dashboard_files/libs/quarto-dashboard/quarto-dashboard.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-dashboard/stickythead.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-dashboard/datatables.min.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-dashboard/pdfmake.min.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-dashboard/vfs_fonts.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-dashboard/web-components.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-dashboard/components.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-dashboard/datatables.min.css [WARNING] Could not fetch resource dashboard_files/figure-html/cell-5-output-1.png

Steps to reproduce

quarto render dashboard.qmd --to dashboard --execute --output index.html -M self-contained:True

Expected behavior

Hopefully the output would look the same as when "--to dashboard" is not used and format: "dashboard" is used yaml.

Actual behavior

The output is missing a lot of resources.
[WARNING] Could not fetch resource dashboard_files/libs/clipboard/clipboard.min.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-html/quarto.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-html/popper.min.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-html/tippy.umd.min.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-html/anchor.min.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-html/tippy.css [WARNING] Could not fetch resource dashboard_files/libs/quarto-html/quarto-syntax-highlighting.css [WARNING] Could not fetch resource dashboard_files/libs/bootstrap/bootstrap.min.js [WARNING] Could not fetch resource dashboard_files/libs/bootstrap/bootstrap-icons.css [WARNING] Could not fetch resource dashboard_files/libs/bootstrap/bootstrap.min.css [WARNING] Could not fetch resource dashboard_files/libs/quarto-dashboard/quarto-dashboard.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-dashboard/stickythead.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-dashboard/datatables.min.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-dashboard/pdfmake.min.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-dashboard/vfs_fonts.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-dashboard/web-components.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-dashboard/components.js [WARNING] Could not fetch resource dashboard_files/libs/quarto-dashboard/datatables.min.css [WARNING] Could not fetch resource dashboard_files/figure-html/cell-5-output-1.png

Your environment

No response

Quarto check output

`Quarto 1.4.538
[✓] Checking versions of quarto binary dependencies...
Pandoc version 3.1.11: OK
Dart Sass version 1.69.5: OK
Deno version 1.37.2: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
Version: 1.4.538
Path: /home/user/opt/quarto-1.4.538/bin

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

[✓] Checking LaTeX....................OK
Tex: (not detected)

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

[✓] Checking Python 3 installation....OK
Version: 3.10.12 (Conda)
Path: /home/user/miniconda3/envs/env/bin/python
Jupyter: 5.3.1
Kernels: python3

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

[✓] Checking R installation...........(None)

  Unable to locate an installed version of R.
  Install R from https://cloud.r-project.org/`

Reproduce the issue with quarto render dashboard.qmd --to dashboard --execute --output index.html -M self-contained:True, then trace the embed-resources handling for renders from a non-input directory. Done means the dashboard output includes the listed JavaScript, CSS, and image resources without fetch warnings and matches the YAML format: dashboard result.