Because DUE's reset connects NRSTB pin, pressing reset will reset the chip including the Backup region (RTC, RTT and Supply Controller), that means RTC's time will be set 2007.1.1 and etc. But in SAM3x, there is another NRST Pin, if reset connect this pin, it will not reset the Backup region (RTC, RTTand Supply Controller), thus, I suggest arduino due make some changes to avoid the RTC's reset.
Not on the actually Due it's how you say it. It's more than hardcoded it's wired on the board itself. Only with a jumper on the next Version to choose there will be no chance of changing.