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Although not elaborated in the documentation, only alluded to, @Begin(flushMode=FlushModeType.MANUAL) only pertains to entity change operations, it does not apply to persisting entities. The main reason for this is identity generation. Certain changes can not be queued in the EntityManager without prior knowledge of the id of an Entity, therefore, when persisting an Entity, the operation must happen immediately and can't be queued.

For this reason, when setting MANUAL flushMode, you will always see persist operations happen regardless of a flush, this is expected behaviour.