Change WordPress theme root to a folder in your plugin (src/assets)

change-theme-root.php

<?php
/**
 * Sample use:
 * 	WordPres Customizer is dependant on functionality in the theme. Just in case
 * 	the current theme doesn't support WordPress Customizer we'll use a theme
 * 	that supports it.
 */
class NN {

	private $theme_name = 'twentysixteen';
	private $plugin_root;
	private $plugin_url;

	public function init() {
		$this->plugin_root = plugin_dir_path( __FILE__ );
		$this->plugin_url = plugins_url( '', dirname( __FILE__ ) ); // note: '' appends a slash to the url
		
		add_action( 'setup_theme', function() {
			add_filter( 'theme_root', array( $this, 'switch_theme_root_path' ) );
			add_filter( 'template_directory_uri', array( $this, 'switch_template_directory_uri' ) );
			add_filter( 'stylesheet_uri', array( $this, 'switch_template_directory_uri' ) );
			add_filter( 'pre_option_stylesheet', function(){
				return $this->theme_name;
			} );
			add_filter( 'pre_option_template', function(){
				return $this->theme_name;
			} );
		} );
	}

	public function switch_theme_root_path( $org_theme_root ) {
		$current_theme = wp_get_theme( $this->theme_name );
		// if theme exists, no point in changing theme root.
		if ( $current_theme->exists() ) {
			return $org_theme_root;
		}

		$new_theme_root = $this->plugin_root  . 'src/assets';
		# Too early to use register_theme_directory()
		if ( ! in_array( $new_theme_root, $GLOBALS['wp_theme_directories'] ) ) {
			$GLOBALS['wp_theme_directories'][] = $new_theme_root;
		}

		return $new_theme_root;
	}
	
	public function switch_template_directory_uri( $template_dir_uri  ) {
		$new_theme_root_uri = $this->plugin_url . 'src/assets/' . $this->theme_name;
		return $new_theme_root_uri;
	}
}

Found a "small" bug, switching theme root worked fine, but in customizer I couldn't save my changes (got "Cheatin' uh?"). Fixed it by applying the filters during setup_theme.

Added missing template_directory_uri

Added missing stylesheet_uri