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What's wrong with using the full operating range of the TIA / ADC instead of the recommended range of half ? (using AFE4490)

Other Parts Discussed in Thread: AFE4490

There are times during which the ADC output signal went very far below 0v and was floating around -500mV before the gain calibration algorithm corrected it to be back in the right range ( >0v, < 1.2v). There didn't seem to be any damage to the signal, and the freq domain analysis was unaffected during the time the ADC output was < 0v. I now want to allow the ADC output, x,  to operate in the range [ -500mV < x < 500mV ]. This is partly because I  want to keep as far away from the saturation values as I can but still be able to amplify the incoming optical signal. 

Does anyone anticipate a problem with this? The case that the datasheet makes for using half the range is not convincing, quoted below:

...because the PPG is one-sided, only half the of the full-scale is used.