How to include all files within a folder & its sub folders to functions.php?

You need to use some recursion on the function:

function require_all_files($dir) {
    foreach( glob( "$dir/*" ) as $path ){
        if ( preg_match( '/\.php$/', $path ) ) {
            require_once $path;  // it's a PHP file so just require it
        } elseif ( is_dir( $path ) ) {
            require_all_files( $path );  // it's a subdir, so call the same function for this subdir
        }
    }
}

require_all_files( get_template_directory() . "/Functions_Folder" );