Using an external programmer (the onboard "Atmel EDBG" in this case) and "Upload using programmer" to program the "Blink" example does not result in a running program.
We also have a non-arduino board with a SAMD21 and "Upload using programmer" with an "ATMEL ICE" does not work either.
It seems like the bootloader initializes partly or in whole the SAMD21 chip, as in both cases, programming the bootloader with Arduino and then using Atmel Studio to program the ELF-file WITHOUT erasing the program memory (so the bootloader is left in memory), then the blink program works on both the ZERO and on our non-arduino board.
Also, "Export compiled binary" exports a BIN-file, instead of a ELF or HEX file as it does for other Arduino boards.
Note: We are actually using "M0 Pro" boards, as we still are unable to buy "Arduino/Genuino Zero" board in europe.