A general note: A lot of things in WordPress can be configured. For example the name of the wp-content directory. The same goes for the name of the plugins and themes directory. And both can have multiple folders (with plugins defining them).
About child themes and plugins: A plugin and a theme is (in general) pretty much the same thing. The (main) difference just is where they get loaded and which info they have for WordPress (in comment headers). And they aren’t connected structurally. So a child theme has nothing to do with a plugin.
Simple rule:
A plugin adds functionality. A theme adds visual representation.
Keeping this separated makes the theme easily exchangeable – and single functionality (each wrapped in a single plugin) as well.
About matching structure from parent > child theme: Yes, you will have to recreate that structure. But only if child theme inheritance is built into the parent theme. For e.g. a stylesheet loaded with get_template_directory_uri() will only load from the parent theme, while the _stylsheet_() counter part will use the one from the child theme. Things like get_header(), get_sidebar(), get_footer() or get_template_part() will search in the child theme first. And a child themes functions.php is also loaded before the parent themes functions.php file.