A serial port is essential for debugging. But if the USB-Port is provided using a USB-to-Serial-Converter this converter needs to be powered form the USB-Bus (and thus from the external control-server). If it is powered from the Embedded Device it would reset during a power cycle and the USB-enumeration could talk longer than the boot of the bootloader.
If an FTDI or similar is used there are usually spare GPIOs available.
Add a note that these GPIOs could be used to switch power of the device or change the boot mode of the CPU, etc.