Hi,
If you just want to run the RTC, in the case, it is okay that you can just connect the VBAT_PMU to a battery or super CAP, the VBAT_DCDC is not powered.
It is okay that you connect the VBAT_PMU to a battery or super CAP, the VBAT_DCDC is powered with 3.3V power supply, but the LPC55S16 is in power down or deep power down mode, in the case, the RTC can generate event to wake-up the LPC55S16.
Hope it can help you
BR
XiangJun Rong