Varying the reference position in `quarto-journals` template

Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2009

@dragonstyle You should read to the bottom of the discussion to see the clearest explanation of what the bug is.

^{Originally posted by sammo3182 August 19, 2022}
Recently I asked a question about varying the reference allocation with Quarto in #1728. Then I find the problem that made the old rmarkdown tricks not work was because I used the article-format-template. The reference was in the right place I want when rendering the plain pdf but then moved to the very end of the document when rendering the aft.

A replicable example:

---
format:
  pdf:
    number-sections: true
  aft-pdf:
    keep-tex: true  
  aft-html: default

bibliography: bio.bib
title:  A test
---

content @Hu2020

# Reference

::: {#refs}
:::

# Online Supplementary Materials

bio.zip

See the difference of the reference when choosing the following options respectively:

How could I allow the aft to recognize my reference setting? Any suggestion will be very helpful.
Moreover, a more detailed instruction and examples about how to customize the template than the current brief version under aft repo and Quarto.org will be super welcomed---details like how to arrange the author area, showing the corresponding author, adding the key words and acknowledge, etc.

Start by reading discussion #2009 to the end, then render the provided QMD example with the plain PDF and aft formats and compare where the references appear. Done means the aft template honors the requested reference position, with the customization guidance and examples requested in the issue addressed or clearly documented.