Breaks the message module

Problem/Motivation

Initially I filed this in the message issue queue 🐛 QueryException: Entity queries must explicitly set whether the query should be access checked or not. Active yet on further inspection it turns out that having entity_clone enabled, breaks message entities (even if those are not cloned in the first place).

Steps to reproduce

- Install entity_clone
- Install the message module and message_ui module
- Create a message entity type, hit save
- Now edit the message entity type, hit save again, and the site will crash with error:
Drupal\Core\Entity\Query\QueryInterface::accessCheck(). in Drupal\Core\Entity\Query\Sql\Query->prepare() (line 141 of /var/www/XXX/core/lib/Drupal/Core/Entity/Query/Sql/Query.php).