-

<?php

namespace AppBundle\Controller;

use Sensio\Bundle\FrameworkExtraBundle\Configuration\Route;
use Symfony\Bundle\FrameworkBundle\Controller\Controller;
use Symfony\Component\HttpFoundation\Request;
use Symfony\Component\Form\FormEvents;

class DefaultController extends Controller
{
    /**
     * @Route("/", name="homepage")
     */
    public function indexAction(Request $request)
    {
        $opt1 = new Opt(1);
        $opt2 = new Opt(2);
        $opt3 = new Opt(3);
        $form = $this->createFormBuilder()
            ->addEventListener(FormEvents::PRE_SUBMIT, function($event) use($opt1, $opt2, $opt3) {
                $event->getForm()
                    ->add('sub', 'choice', [
                        'multiple' => true,
                        'expanded' => true,
                        'choices_as_values' => true,
                        'choice_label' => 'label',
                        'choice_value' => 'id',
                        'choices' => [$opt1, $opt2, $opt3],
                        'data' => [$opt1, $opt3],
                    ])
                ;
            })
            ->add('submit', 'submit')
            ->getForm()
        ;
        $form->handleRequest($request);
        return $this->render('default/index.html.twig', array(
            'form' => $form->createView(),
        ));
    }
}

class Opt {
    public $id;
    public $label;
    public function __construct($id)
    {
        $this->id = $id;
        $this->label = "label for $id";
    }
}

@webmozart when a choice is is added via a (PRE_SUBMIT) listener, data isn't taken into account, and checkboxes aren't pre-selected.

Really? Interesting.. this should work IMO. Can you create a reproducible symfony-standard branch and open a ticket?