1)¶

The [] Enable auto-suggest for taxon search is currently in the freetext index settings.

This option should preferably be placed below:

admin/config/cdm_dataportal/settings/layout/search#edit-simple-search-use-lucene-backend

2)¶

Harmonize the Drupal value key:

please rename the key cdm-dataportal-taxon-auto-suggest to something that better conforms to the existing keys of the same context. My suggesting is: cdm_search_taxa_auto_suggest.
The existing implementations in settings.php may be a good guidance:

   define('SIMPLE_SEARCH_IGNORE_CLASSIFICATION', 'simple_search_ignore_classification');

...

    $form['search_settings'][SIMPLE_SEARCH_IGNORE_CLASSIFICATION] = array(
      '#type' => 'checkbox',
      '#title' => t('Ignore the chosen classification in simple search'),
      '#default_value' => variable_get(SIMPLE_SEARCH_IGNORE_CLASSIFICATION, 0),
      '#description' => t('The simple search, which can be executed via the search block,
          will by default search on the classification selected in the classification browser
          selector. Set the tick if you want your portal to search on all classifications.'),
  );