Hi,
.what is the difference between software watchdog timer and MCU core watchdog timer?
It is quite well described in following appnote, chapter 4.1.8:
http://cache.freescale.com/files/analog/doc/app_note/AN4113.pdf
Both watchdog are present on the device due to backward compatibility with MPC55xx, but SWT offers advanced features. Note that MPC5644A and MPC5674F has it implemented same way.