Focusing on the new 'enhancement' and not maintaining the old instrumentation is fine.
At the same time, I would expect that the old 'instrumentation' to behave as it did before 5.0. So it would be OK that if there were bugs before those would not be fixed.
In this case though the bug was introduced in 5.0. This is a regression.

About the 'enhancement', is this documented somewhere ? I did find this page by chance (https://docs.jboss.org/hibernate/orm/5.0/topical/html/bytecode/BytecodeEnhancement.html) where I learned that you can pass options to the maven plugin. But it is still short on details.
Initially, when doing some testing of the enhancement using the maven plugin, I was not providing those options and 'enableAssociationManagement' was true (I think that this is the default value). This leads to some 'unexpected' (at least to me) behavior like trying to persist an entity because of an autoflush before it was fully initialized.
I also had the same issue than the one described in

Do not get me wrong, I will try to use the new enhancement as much as possible as long I am not bitten by other issues.
Which I had today while doing some other tests about LAZY properties. I will open another ticket for this 'new' issue (but it may as well be 'an operator error')