If you are using the circuit diagram ATM90E32AS_3P4W_CT.SchDoc, you will get 240 mV rms at 100 A current. The maximum input voltage is 720 mV, therefore you should set the PGA_GAIN to 2 (according to the Application Note). If you will be measuring not more than 75 A, you can set the PGA_GAIN to 4.
On page 8 of the Application Note, it says: “Application note: how to select CT and CT load resistance.” You can choose a current transformer and its burden (load resistance) to suit the current you want to measure. Ideally, the voltage that appears across the burden resistance will be just less than 720 mV at the maximum current that you want to measure.
If it is much less than this - as it is for you - you can set the amplifier gain to compensate.
Atmel do not know which current transformer you will be using, nor what the value of burden resistance you will have chosen. They cannot tell you what numbers to use in the calibration registers.
You adjust for your choice of components by setting values in the calibration registers. If the number is incorrect, the current that the ATM90E32 indicates will be wrong, and the power and energy will be wrong.