The IoT pHAT needs a GPIO to reset the WiFi when using the "reboot" command, so the gpio-poweroff overlay is used.
However, when using "poweroff" or "halt" command, it (the gpio-poweroff overlay) will cause the kernel panic at the end, there are some discussions in Raspberry Pi forum but no exact answer or solution for this.
Actually, it will not harm your system, also you still need to cut the power manually.
If you really want to shutdown the system gracefully (maybe for your own product):
1. you need make use of the systemd to drive low to the GPIO pin to WL_REG_ON (pull low to turn off the WiFi).
2. remove the gpio-overlay in the EEPROM source file,
Any good suggestions are welcome.