[Docs request] Workflow for working with academic templates

I've been testing teaching using Journal templates for Quarto, but I keep hitting the same issue every time:
What is the best workflow for using a template, knowing you are likely to switch to another template at a later stage?

Academic publishing often leads us into several rejections from various journals, meaning the need to switch template.
But I have yet to find a workflow that I find particularly satisfying to recommend.

I usually start with recommending to quarto use template as this provides also a template.qmd to start filling in, often with useful links to journal publishing guidelines. This, however, forces the use of a sub-directory, and the need to either:

1. move _extensions folder to the project root for use with the main doc and possibility to add more extension + transfer the template yaml to your document and start adapting
2. copy your document content to the template.qmd and adapt the yaml + do the same for every new extension, overpopulating the the project with unnecessary sub-directories.

Having the template.qmd is so very useful to know what yaml options the template has or needs, but the subdirectory (though understamdably needed) makes a messy project.

When trying to show the second way of installing a template quarto install extension the project structure is nicely maintained, but there is not template.qmd to aid in yaml option settings. It requires exploring the root repo the template is in on github and opening the qmd there to see the tempalte. This is not so convenient.

Do you have any recommendations for how a workflow for this would look like?

Start by comparing the quarto use template and quarto install extension workflows, including the generated template.qmd, _extensions directory, and template YAML options. Document a recommended workflow for switching academic templates while keeping the project structure manageable and preserving access to template guidance.