Atomic transactions reduce persistence points. Those are when the Orchestration saves it state back to the database.
Depending on how you are looping, you could see poor performance due to the persistence points.
Are you XPathing out the message to map within the loop?
Without seeing your Orchestration, it’s hard to say what’s really causing the problem.
All in all, I do not think you will match or even come close to the pure .net component in this scenario.