Rabbits do not like being picked up. As a prey species, being picked up means they are about to be eaten (to their instincts). Usually when they are sitting “calmly” while held, it is because they are afraid and uncomfortable, rather than content and happy to be held. Frequently picking up a rabbit can cause trust issues and … well thumping and sometimes biting. They are not cuddly animals, in general. And if he is unable to always hold her the “right way” that will just increase her distrust. A thump in rabbit language would mean “no” or “stop”.
A way she would probably enjoy being interacted with more is him laying on the floor with her and letting her come to him. He can offer her treats and lie still and let her climb over him.
Now, this doesn’t mean you can never pick up a rabbit. But, generally it is best to only do it as much as you need to. Grooming, clipping, vet visits, etc. She should be able to be picked up, so pick her up often enough she is used to it and allows it in case of emergency… but not enough that she thinks he is always going to be grabbing her. 