What's the purpose of subfolders inside a theme's templates folder? What is the purpose of folders inside the templates folder in a theme? Where is specified that when rendering a page the template should be taken from layout/page.html.twig? Or a single node template from content/node.html.twig?

I could see content, block, field, form etc. in the /templates folder. I am referring to the Zymphonies theme. When I check Twig Template naming conventions I could see there are naming conventions for Twig templates. But what is the difference in giving Twig plain twig templates inside the templates folder and by giving specific twig templates in specific folders inside templates folder?
These folders are arbitrary. As long as the template is in the [THEME ROOT]/templates folder, it will be picked up. Using folders is simply the developer being well organized.