Sorry, a bit late to this one. Unless the threads are damaged, it will sit perfectly nice. It's the exact same set up I'm using now. Are you able to push the entire brass and copper connection out of the top cap? If this is somehow stuck, it won't sit flush.
Best way to mount any topper is to remove the top cap, ensure the brass part of the contact is pushed right the way in, then screw your topper down. You should see the pin get pushed back slightly. Only now do you need to adjust the copper screw to make contact with the battery. If I try and put the Atomic straight on after using another RDA, it won't sit flush as it can't move the pin back any more as it's against the battery.