why does EntityForm::copyFormValuesToEntity() specifically not copy form values for a plugin collection?

I have a config entity type, which works with a single plugin, and thus uses DefaultSingleLazyPluginCollection.

The entity form for this gets form elements from the selected plugin, and then the form values should get saved into the entity.

However, copyFormValuesToEntity specifically stops this from happening:

  protected function copyFormValuesToEntity(EntityInterface $entity, array $form, FormStateInterface $form_state) {
    $values = $form_state->getValues();

    if ($this->entity instanceof EntityWithPluginCollectionInterface) {
      // Do not manually update values represented by plugin collections.
      $values = array_diff_key($values, $this->entity->getPluginCollections());
    }

The keys of getPluginCollections() are the entity properties that store plugin configuration.

Am I doing something wrong in the way I am building a config entity + plugin combination?