To speak SWD, I just use the Atmel-Ice programmer, and Atmel Studio 7 (a windows application, sorry). Any programmer that speaks SWD should be capable of doing this. In Atmel Studio, go to `Tools -> Device Programming`, and select the Atmel-Ice Tool, the ATSAMD51xxxx device you'd like to program (the bootloader is written for the ATSAMD51J19A), and the SWD interface. You should be able to read the device signature. If this works, your SWD connection is all super-gucci (as they say). You can navigate to `Memories` - and write that bootloader in. OK. The device should now enumerate over USB as an Adafruit Feather M4 / FeatherBoot (or something similar).
I haven't tried this yet, but you should be able to do the same thing Jake did for the