As I said previously, there is no problem reading/writing any of the Atmega registers with Arduino code if there is no "helper" function for the task.
I'm interested to learn with you.
Are you saying the 2560 can accept an AC signal with positive and negative voltages (referred to Arduino GND) and (for example) an ADC value of 20 might represent -4.8v and 1000 might represent +4.8v?
What is the max negative voltage that is accepted without letting the smoke out?
OR ... does differential just mean the difference in voltage between a pair of ADC pins - to save you having to take two ADC readinsg and subtract the results?
I notice that the Leonardo seems to have the same facility.
....R
Edit. I found this and I have crossed out the "wrong" assumption above. YouTube video
...R