When you turn ON the “Force custom post types to use their own capabilities” option at “User Role Editor Pro” settings “Additional Modules” page:

force custom post type use own capabilities
Force custom post type to use own user capabilities

URE applies it to all existing custom post types and related custom taxonomies. If you need to exclude some taxonomy from this action, leave the default capabilities for selected taxonomy, use the 'ure_set_cpt_taxonomy_own_caps' filter, like at the example below, which leaves the default capabilities for WooCommerce product categories:

add_filter( 'ure_set_cpt_taxonomy_own_caps', 'set_cpt_taxonomy_own_caps', 10, 3 );
 * @param bool $do_it (TRUE by default)
 * @param string $taxonomy (like 'product_cat', etc.) 
 * @param string $post_type (like 'product', etc.) 
 * @return bool
function set_cpt_taxonomy_own_caps( $do_it, $taxonomy, $post_type ) {
    if ( $post_type==='product' && $taxonomy==='product_cat' ) {
        $do_it = false;
    return $do_it;

This filter is available from version 4.59.3