XCTU will not find the radio despite the HCS08 bypass because the firmware flashed has not a serial port.
The solution is to flash the latest bootloader and hit option & (it's not shown in the default menu). This option performs a bypass that also propagates the reset line, that way you should be able to enter the radio's bootloader (same steps for HCS08 bootloader, break line, reset, clear break). Once in the ember bootloader, XCTU should let you flash a new firmware.
Note that because the reset line is propagated the only way to revert the "&" bypass is to cycle power.