Solved it after some trial and error.
Turns out the third party ST Link V2 I have, has to be unplugged and replugged into the USB which presumably puts it into the correct mode. Then, holding down the RST button on the Lora E5 Mini dev board, clicking Connect on the STM32CUBEProgrammer software and releasing the RST button, allows the board to be detected and programmed every time.
This is on a macbook pro running Big Sur (11.2.3) using a Yootech USB-C to USB adaptor. The Lora E5 Mini is also connected via USB with an Arduino Serial Monitor open to view its output. The dev board is wired up according these instructions: https://wiki.seeedstudio.com/LoRa_E5_mini/#2-develop-with-stm32cube-mcu-package
Now to actually write some code for it!