Entity "changed" timestamp is not incremented on $entity->save() only on a form submit; feature or bug? Anyone know why the changed timestamp is not updated when you save an entity programmatically (e.g. $entity->save()) but it is updated when you (for example) use the node form to edit the entity. 

Is this intentional? If so, why?

If not, I'll open an issue on D.O.

Thoughts?
Pretty sure it is being updated, but it is updated to the REQUEST_TIME timestamp. If you have a long-running process or so, that will not work as expected.