This is the code in 5.3.1:
https://github.com/hibernate/hibernate-orm/blob/5.3.1/hibernate-core/src/main/java/org/hibernate/internal/AbstractSharedSessionContract.java#L934

It did not contain the filter you're talking about. In my commit I simply reverted a change that has been introduced in 5.3.2 and had unwanted side effects.

So if you have code that was working prior to 5.3.2 but is not working with 5.3.3, please provide a test case as there might be an issue different from what you suspect.

Thanks!