I am on WP version 5.5.3 and I have added the following code to my child theme functions.php.

function my_targeted_link_rel($rel_values) {
 	return 'noopener';
}
add_filter('wp_targeted_link_rel', 'my_targeted_link_rel',999);

However, Gutenberg is still adding noreferrer when I create a new link that opens in a new tab. Where is this coming from?

I don't think it's necessary to hard code rel attributes into the link module. Just let wp_targeted_link_rel add the necessary rel attributes when the post is saved/updated.