It's my impression that the crystal arrangement really refers to the distribution of ions in the trap. Exciting one atom does add energy to the system, but in a

It's my impression that the crystal arrangement really refers to the distribution of ions in the trap. Exciting one atom does add energy to the system, but in a near-eigenstate that's quite orthogonal to the crystal's structure. Whether the distinguishability of one ion over the others changes the quantum statistics is an important and subtle problem. You're right to be skeptical. When the time comes to interpret the results of this experiment, you'll find yourself in good company. Doubly so if the experiment resolves T violation.