I flash my firmware using openocd and an STM32 "Blue Pill" flashed to the CMSIS-DAP firmware.  I use openocd to flash a bin file that contains both the UF2 bootloader as well as the fusee firmware.  It's a bit more convenient to do it all in one shot than to flash the bootloader first and then switch to USB or arduino for the firmware.  After this initial programming, I use the USB virtual flash drive from the UF2 bootloader to modify or change firmware as openocd is no longer needed.

For this project, I just use the blue pill to directly contact the four programming pads I placed on the SAMD board.  A little bend in the blue pill headers give a nice springy connection that I can pop on and use to hold the board steady while flashing.  This initial flash takes about 30 seconds, so it's pretty quick to do a batch of 10 or 20.