Filter the Genesis CPT breadcrumb for hierarchical CPT to include ancestor pages.

genesis.php

/**
 * Filter the Genesis CPT breadcrumb.
 *
 * @since 2.5.0
 *
 * @param string $crumb HTML markup for the CPT breadcrumb.
 * @param array  $args  Arguments used to generate the breadcrumbs. Documented in Genesis_Breadcrumbs::get_output().
 */
function nn_cpt_breadcrumb( $crumb, $args ) {
  global $wp_query;

  if ( !is_singular( 'CPT_SLUG' ) ) {
    return $crumb;
  }

  $post = $wp_query->get_queried_object();

  // If this is a top level Page, it's simple to output the breadcrumb.
  if ( ! $post->post_parent ) {
    $crumb = get_the_title();
  } else {
    // Get the IDs of all parents and ancestors in an array.
    $ancestors = get_post_ancestors( $post->ID );

    // Add ancestor breacrumb links to $crumbs array
    // get_breadcrumb_link() https://gist.github.com/natenault/af861546ab8a3468d12a09e89437ed54
    $crumbs = array();
    foreach ( $ancestors as $ancestor ) {
      array_unshift(
        $crumbs,
        nn_get_breadcrumb_link( get_permalink( $ancestor ), '', get_the_title( $ancestor ) )
      );
    }

    // Add the current page title.
    $crumbs[] = get_the_title( $post->ID );

    $crumb = implode( $args['sep'], $crumbs );
  }

  return $crumb;
}
add_filter( 'genesis_cpt_crumb', 'nn_cpt_breadcrumb', 10, 2 );