Plugins, like any other functions file in a theme are just extensions to your theme’s functions.php file. Any file that extends the main functions.php has to be manually included into the main functions file. The reason for this is, only files and templates within WordPress file structure gets auto laoded. There is no logic to regocnize and to include custom files or templates
The main plugin file of a plugin however is autoloaded and need not to be manually included, although it is just an extension to the main functions.php file of your theme. A plugin is identified by the header of the main plugin file, and it is this header that wordpress uses to identify the plugin and according to that auto loads the main plugin file.
Again, WordPress only loads the main plugin file as it only knows this file. Any extension to the main plugin file is ignored as WordPress don’t recognize it. To get WordPress to load any other files, you need to include them into the main plugin file