Use Yoast SEO (WordPress plugin) Primary Category only on Category taxonomy.

yoast_filter_primary_tax.php

<?php
/* Use Yoast SEO's Primary Category feature only on Categories. */
function myprefix_yoast_primary_tax( $all_taxonomies ) {
    $args = array( 'name' => 'category' );
    $all_taxonomies = get_taxonomies( $args, 'objects' );
    return $all_taxonomies;
}
add_filter('wpseo_primary_term_taxonomies', 'myprefix_yoast_primary_tax' );
?>

Yoast defaults to using its Primary Category feature on all hierarchical taxonomies, including custom ones. This script uses the plugin's filter (/admin/class-primary-term-admin.php) to return only the object for the 'category' taxonomy, thereby applying the feature only to that taxonomy.