Is it correct, that I can use the Arduino/Genuino Zero Bootloader?
If yes, can I programm the micro-controller using the native USB-Port?
Looks like the source code contains everything you need to get the SAMD21J set-up and running with the Arduino IDE.
Can I reflash the bootloader through the Arduino IDE with the ATMEL-ICE?
But, the bootloader they use in the demo won't load on the Sparkfun SAMD21 Mini Breakout. It said the file type was incompatible. That got me confused that it was .hex vs. a .bin issue. But in the end, it must have been something else. Sparkfun doesn't have a .hex of their bootloader available and looked like I was going to have to compile my own. But, the Adafruit Feather m0 bootloader worked fine.