So, I went ahead and tried to figure out a fix. I wanted to work against 4.3 because if I have to run my own fork for a while, I want to use that baseline. I got a fix (I think), but when I tried to port that fix over to master, I couldn't – the SecondPass mechanism has changed and I couldn't see where it lives now.
So here's the test and fix PR for 4.3:
https://github.com/hibernate/hibernate-orm/pull/751
and here's the test and incomplete fix PR for master:
https://github.com/hibernate/hibernate-orm/pull/752