These are physics tools for specific things, not general radio receivers for transmitted information.
Antenna are about capturing energy over macro scale areas. This atom is measuring electromagnetic oscillation at a particular point in space. Technically you can recover a signal, but only a rounding error above the noise floor. It doesn't capture energy.
This is important because previously it was possible to measure accurately either lower frequencies, until a few hundred GHz, or higher frequencies, from infrared to ultraviolet, i.e. from tens of THz to hundreds of THz.
Measuring accurately frequencies allows accurate spectroscopy in this frequency range, which can provide information about the chemical composition of materials.
'Frequency combs" are devices that can do at much higher frequencies what digital frequency dividers can do at low frequencies, and this frequency division function is what allows frequency measurement, by converting the high-frequency signals into low-frequency signals, whose frequency can be measured with the classic methods.
The method described in the article has the additional advantage of high sensitivity, i.e. it can measure very weak signals, which could not be distinguished from noise by less sensitive methods.
TFA mentions spectroscopy and non-destructive scanning instead of X-rays.