So I found the key reason for the problem after fiddling with the spring attached project. The issue is one of configuration:

<prop key="hibernate.order_inserts">true</prop>
<prop key="hibernate.order_updates">true</prop>

When specifying these settings is when the constraint violation occurs. Replicating those into my test case makes it fail as well, so it is indeed a Hibernate issue at least. I'll continue from there.