Uncaught PHP Exception InvalidArgumentException: "Value is not a valid entity."

Does this actually work?

While the PHP error is gone, the payment reference target_id returned seems to be 0, which is not helpful either.

Is the problem that the payment is not saved, so we have no payment id?

This actually seems to return an array:

array (
  'container' => 
  array (
    'payment_form' => 
    array (
      'payment_method' => 
      array (
        'container' => 
        array (
          'select' => 
          array (
            'container' => 
            array (
              'plugin_id' => 'payment_basic:cheque',
            ),
          ),
        ),
      ),
    ),
  ),
)

So how would I actually get to the value of the saved payment?

I seem to be able to get the right target_id from:

$form_state->getStorage()['payment_reference.element.payment_reference.payment']->id();