Index configurations are changing from export to export.

Nothing to do here, indeed but the issue is very annoying and 📌 Add orderby key to all sequences in core Active might take years until is fixed. Here's a workaround to whom it may concern:

/**
 * Implements hook_ENTITY_TYPE_presave() for search_api_index entity type.
 *
 * On each config export, the Search API indexes dependencies are shuffled. This
 * is just a workaround until #2855675 is fixed.
 * @see https://www.drupal.org/i/2855675
 * @todo Remove this when https://www.drupal.org/i/2855675 lands.
 */
function mymodule_search_api_index_presave(IndexInterface $index): void {
  $sorted = [];
  foreach ($index->getDependencies() as $type => $dependencies) {
    sort($dependencies);
    $sorted[$type] = $dependencies;
  }
  $index->set('dependencies', $sorted);
}