This is merely a speculation but could it be explained by some circuitry between the battery terminals and the point where the voltage is measured? If the difference stays contact at different charge levels, that would be a good indicator.
Of course the bigger battery charges slower, it is double the capacity! A twice as large bucket will also take twice as long to fill up from the same tap. I am not sure what you mean by charger+-. The phone is charged through the USB port, right? Do you mean cutting the USB wires and connecting them directly to the battery terminals? That would be a sure way of killing the battery (and maybe losing an eye in the process, if the battery explodes in your face).