It seems I can get what I'm after by rendering just the prototype attribute of my form's collection field, this feels like the long way around, but it works.
// Controller method
$form = $this->createForm(new MyType());
$view = $form->createView()->children['myCollection'];
$prototype = $this->renderView('MyBundle:Foo:prototype.html.twig', array('form' => $view));
<!-- Template (MyBundle:Foo:prototype.html.twig) -->
{{ form_widget(form.vars.prototype) }}