Toggle features?

+1. I was actually just thinking the same thing – the favicons are unnecessary and I’d love to have a way to disable them.

Yes, but not via settings page.
You can use the hook multisite_enhancements_autoload to filter the included classes. Each class have a function.

As example plugin to unset the favicon feature:

You find this code, a example for download also in the dev repository: https://github.com/bueltge/wordpress-multisite-enhancements/wiki/Remove-features

<?php
	/**
	 * Plugin Name: Multisite Enhancements Add-on to remove features
	 * Description: Thhis plugin remove features from the Multisite Enhancement plugin.
	 * Plugin URI:  https://github.com/bueltge/WordPress-Multisite-Enhancements
	 * Version:     2015-12-03
	 * Author:      Frank Bültge
	 * Author URI:  https://bueltge.de
	 * License:     GPLv2+
	 * License URI: ./assets/LICENSE
	 * Text Domain: multisite_enhancements
	 * Domain Path: /languages
	 * Network:     true
	 */

	! defined( 'ABSPATH' ) and exit;

	add_filter( 'multisite_enhancements_autoload', function ( $files ) {

		// Unset the favicon-feature, file class-add-admin-favicon.php.
		unset( $files[ 0 ] );

		/**
		 * Current are this possible.
		 *
		 *  0 => inc/autoload/class-add-admin-favicon.php'
		 *  1 => inc/autoload/class-add-blog-id.php'
		 *  2 => inc/autoload/class-add-plugin-list.php'
		 *  3 => inc/autoload/class-add-site-status-labels.php'
		 *  4 => inc/autoload/class-add-theme-list.php'
		 *  5 => inc/autoload/class-admin-bar-tweaks.php'
		 *  6 => inc/autoload/class-change-footer-text.php'
		 *  7 => inc/autoload/class-core.php'
		 *  8 => inc/autoload/class-filtering-plugins.php'
		 *  9 => inc/autoload/class-multisite-add-new-plugin.php'
		 * 10 => inc/autoload/core.php'
		 */

		return $files;
	} );