How do you programmatically include an entity type to a workflow?
You need the addEntityTypeAndBundle method from ContentModerationInterface 

A static way to implement it looks like:

$workflow = \Drupal::entityManager()-&gt;getStorage('workflow')-&gt;load([workflow_id]);

$workflow-&gt;getTypePlugin()-&gt;addEntityTypeAndBundle('node', 'article');

$workflow-&gt;save();