Solution to https://www.drupal.org/node/2706057

EntityReferenceDefaultValue.php

<?php
/**
 * @file
 * Contains \Drupal\mymodule\Feeds\Target\EntityReferenceDefaultValue.
 */

namespace Drupal\mymodule\Feeds\Target;

use Drupal\Core\Form\FormStateInterface;
use Drupal\feeds\Exception\EmptyFeedException;
use Drupal\feeds\Feeds\Target\EntityReference;

/**
 * Decorates the entity reference target with a default value field.
 *
 * @FeedsTarget(
 *   id = "mymodule_entity_reference",
 *   field_types = {"entity_reference"},
 *   arguments = {"@entity.manager", "@entity.query"}
 * )
 */
class EntityReferenceDefaultValue extends EntityReference {

  /**
   * {@inheritdoc}
   */
  protected function prepareValue($delta, array &$values) {
    try {
      parent::prepareValue($delta, $values);
    }
    catch (EmptyFeedException $e) {
      if (!empty($this->configuration['default_value'])) {
        $values['target_id'] = $this->configuration['default_value'];
        return;
      }
    }

    throw new EmptyFeedException('No default value');
  }

  /**
   * {@inheritdoc}
   */
  public function defaultConfiguration() {
    return parent::defaultConfiguration() + [
      'default_value' => NULL,
    ];
  }

  /**
   * {@inheritdoc}
   */
  public function buildConfigurationForm(array $form, FormStateInterface $form_state) {
    $form = parent::buildConfigurationForm($form, $form_state);

    $form['default_value'] = [
      '#type' => 'textfield',
      '#title' => $this->t('Default target id'),
      '#description' => $this->t('This target id is used if there is no result.'),
    ];

    return $form;
  }

  /**
   * {@inheritdoc}
   */
  public function getSummary() {
    $summary = [parent::getSummary()];

    if (!empty($this->configuration['default_value'])) {
      $summary[] = $this->t('Default target id: ' . $this->configuration['default_value']);
    }

    return implode('<br>', $summary);
  }

}