Setting Simple Sitemap Values Programmatically not reflected in form
I figured this out, but in case anyone else runs into this. The documentation in the readme.md file shows the following format the settings:

setBundleSettings('node', 'page', ['index' =&gt; TRUE, 'priority' = 0.5])

Instead of using TRUE/FALSE I changed the index setting to 0/1 and this was successfully reflected in the form as expected. 

\Drupal::service('simple_sitemap.generator')-&gt;setEntityInstanceSettings('node', $node-&gt;get('nid')-&gt;value, ['index' =&gt; 0]);