Caching and Versioning for rtl.css

You are loading the rtl.css using the WordPress automatic way, that is, having a rtl.css in the theme folder will be loaded by WordPress automatically if it presents and direction of current language ir rtl (you should add this information to the question, it has been difficult to figure it out how you are loading the file). This process defines locale_stylesheet_uri that you can use to modify the locale stylesheet URL, so you can add the version parameter to it:

add_filter( 'locale_stylesheet_uri', function ($localized_stylesheet_uri) {
    $time_ver = filemtime( get_stylesheet_directory() . '/rtl.css' );
    return add_query_arg( array('ver' => $time_ver), $localized_stylesheet_uri );
});

If you need also handle dependencies you will have to load rlt.css file with wp_enqueue_style just like any other css file. No way of handling dependencies with the “auto” way.