oembed creates broken file entities when created anywhere but the wysiwyg popup

I'm working on tests cases for oembed links, to make sure that they all render properly with our filter format. This demands I create file entities programmatically. However, when I do this, they don't get a bundle type set. I'm just calling $handler->save() to create the entity and that gives me broken ones that crash Drupal.

The bundle type is only set in the validators for the media form. If the form is not called with something in its 3rd parameter, the bundle is never set. If the form is not called at all, and the entity created with the handler, the bundle is never set.