That's good, it means that the board and bootloader are working correctly.
Arduino boards that communicate over their native USB port, require a fully functioning sketch to allow auto reset and upload to work correctly. If there's a bug somewhere in the sketch and the microcontroller crashes, the COM port can be lost. The double tap reset to put the microcontroller into bootloader mode, allows the board to be recovered when this happens.
Actually, the bootloader's not too fussy when it comes to selecting the microcontroller variant, since apart from the memory (that you've now accounted for), it's using resources that are common to all of them. I'd just leave the microcontroller type as SAMD21G18A.
Bossa on the other hand, is more thorough and certainly on Shumatech's version it's checking the device ID, which is most likely why it didn't work with your SAMD21E17D variant.
In the "board_definitions_arduino_zero.h" file, if you don't require the status, Tx or Rx LEDs just comment out these lines and the bootloader code will automatically detect this and remove the code to control them.
Apart from the "board_definitions_arduino_zero.h" configuration file, if you only want the native USB upload and not the UART option, change line 65 in the bootloader's "Makefile" from: