I'd prefer to see manual transactions

I understand making the code more clear is good. But since here a lot depends on a particular ORM, ORM-specific code beautifying may lead to opposite effect: people might consider the test as suspicious.
DO4 can do nearly the same: you may not explicitly set transaction boundaries. In this case framework will automatically establish them. What exactly will happen depends on session configuration - e.g. any method call can be wrapped into individual transaction; it may just start it with the first call, but do not commit, and so on. But here we decided to avoid this at all. Just to not confuse the people.
What can be done: if you want to make the code looking more common, you can e.g. extract begin / commit transaction code into a special methods. I.e. anything similar is acceptable. Test must conform with the rules and be easy to understand. That's it.