Example of Yoast update changing custom query vars

sitemap-test.php

<?php
/*
 * Plugin Name: Sitemap Test
 * Description: A simple plugin to test Yoast sitemap integration.
 */

function add_to_yoast_sitemap( $custom_sitemaps ) {
	$custom_sitemaps .= '<sitemap><loc>' . site_url() . '/my-custom-sitemap.xml</loc></sitemap>';

	return $custom_sitemaps;
}

add_filter( 'wpseo_sitemap_index', 'add_to_yoast_sitemap' );

function my_query_vars( $vars ) {

	$vars[] = "xml_my_custom_sitemap";

	return $vars;

}

add_filter( 'query_vars', 'my_query_vars', 15 );

function rewrite_rules() {

	add_rewrite_rule( '^my-custom-sitemap\.xml$', 'index.php?xml_my_custom_sitemap=true', 'top' );

}

add_action( 'init', 'rewrite_rules', 1 );

function generate_my_sitemap() {

	global $wp_query;
	// var_dump($wp_query->query_vars); die;
	if ( ! empty( $wp_query->query_vars["xml_my_custom_sitemap"] ) ) {
		$wp_query->is_404 = false;
		var_dump($wp_query->query_vars); die;
		// Create your sitemap here
	}

}

add_action( 'template_redirect', 'generate_my_sitemap' );