Yes, starting with version 0.4.0 organization of markdown files in subdirectories 'docs/*.md' with extension 'md' under 'docs' folder is possible. With that feature comes the data entry ${data.base}, which is holding the relative path from the current markdown file to the 'docs' folder and can be used in template header sections.

Hmm, you need to ...

1. add or change "math":true/false setting in the frontmatter section of your markdown document.
2. activate (set focus away to) any other editor window (preview window works perfect here).
3. reactivate (set focus back to) your markdown document.
4. make any modification (a simple keystroke should work) and see change in math rendering.

The CSS styles are defined in the file /docs/theme/styles.css. They are referenced by the templates in file /docs/theme/template.js.

Yes. Change them in file /docs/theme/styles.css or rename it or use multiple CSS files. You only need to reference them from the templates in /docs/theme/template.js.

The templates are defined in file /docs/theme/template.js. They are basically delivered by simple JavaScript functions returning template literals. Those recieve extended versions of the frontmatter metadata.

Yes, of course. New themes are generated exactly by that. So go on and do it.

No sorry, it's due to minimalism paradigma.

Yes, it should be easy in principle. Nothing done here yet.