Yoast Seo noindex added to pages outside wordpress

You can use the wpseo_robots filter (yoast documentation) to override that. Add something like

add_filter("wpseo_robots", function() { return "index, follow"; });

before calling get_header() to overwrite what wpseo sets. Don’t put it in the functions.php of your theme, though, or it will be used on everything in WP.