The battery is split into two compartment by which i mean that while using the mobile while charging only one compartment will charge while the other will discharge so the reactons do not heat and destroy the battery
A battery either charges, or discharges. If the phone is used at the same time, there is no problem. Charging one cell while discharging another is a bad idea because it increases the number of cycles of charge/discharge, which is reduces its efficiency and capacity.
And so far, we have survived as a civilization with single-cell batteries :-)
How is it different from using two batteries?