How to list users that have written custom post types and hide the ones that have not?

wp_list_authors(), internally gets posts that are only of type post. See line 294 http://core.trac.wordpress.org/browser/tags/3.2.1/wp-includes/author-template.php#L273

As you have noted, this answer is great and with some modification can do what you want.

function wpse31443_author_has_custom_post_type( $post_author, $post_type ) {
    global $wp_post_types; // If nonexistent post type found return
    if ( array_intersect((array)$post_type, array_keys($wp_post_types))
        != (array)$post_type ) return false;

    static $posts = NULL; // Cache the query internally
    if ( !$posts ) {
        global $wpdb;

        $sql = "SELECT `post_type`, `post_author`, COUNT(*) AS `post_count`".
            " FROM {$wpdb->posts}".
            " WHERE `post_type` NOT IN ('revision', 'nav_menu_item')".
            " AND `post_status` IN ('publish', 'pending')".
            " GROUP BY `post_type`, `post_author`";

        $posts = $wpdb->get_results( $sql );
    }

    foreach( $posts as $post ) {
        if ( $post->post_author == $post_author
            and in_array( $post->post_type, (array)$post_type )
            and $post->post_count ) return true;
    }

    return false;
}

You already know how to get_users, so it should be a piece of cake to setup a simple foreach loop and feed the user IDs into your new function.

I’ve tested the function to some extent, it should work as is, but may require some tweaking. Let me know if you have any questions and/or how I can improve my answer.