Instances are recreated on load

Problem/Motivation

Since #3575913: Compatibility with JSON API, part 2, past and future steps are "lost" at every instance entity load, only present step is loaded. That's why LogsPanel and HistoryButtons are useless now.

Example:

$instance = $storage->load($instance_id);
$load = $instance->toArray();
$first_load = $load;
// ✅ Load has only present
$builder->setNewPresent([], 'empty everything');
$builder->save();
$load = $builder->toArray();
// ✅ Load has 1 past step
$builder->setNewPresent($first_load['present']->data, 'restore everything');
$builder->save();
$load = $builder->toArray();
// ✅ Load has 2 past step
$instance = $storage->load($instance_id);
$load = $builder->toArray();
// ❌ Load has only present

Proposed resolution

Is it because we do an entity creation in an unexpected place from InstanceStorage?

  protected function doLoadMultiple(?array $ids = NULL): array {
    $entities = [];
    ...
    foreach ($ids as $id) {
      if ($data = $this->state->get(self::STORAGE_PREFIX . $id, NULL)) {
        $entities[$id] = Instance::create($data);
      }
    }

    return $entities;
  }

We may need to do an entity object instantiation instead:

$entities[$id] = new Instance($data, 'display_builder_instance');

It was not detected by tests, do we need to add a new one or extend an existing one?