When a theme comes packaged with its own plugins, the end user is instructed to install it in /wpcontent as opposed to the normal /wp-content/themes directory so that plugins and theme files are installed in their appropriate places. You want that separation between form and function.
The theme should include hooks to those plugins, and then the administrator has to activate them after installation.
Packaging your theme like this is effectively what you are trying to do; we are just broadening the definition of a theme a bit to include its plugin directory.
If you are determined to have the plugin directory be a subdirectory of the theme, I'm not sure if or how that's doable, but it is bad practice because it doesn't maintain the separation between form and function.