I am using Atmel-ICE, I have no idea about another way how to program bootloader now!

Arduino > Preferences : Additional boards manager URLs ADD https://www.mattairtech.com/software/arduino/beta/package_MattairTech_index.json

Arduino > Tools > Boards manager : MattairTech MT-D21E (rev B) 

Arduino > Tools > Clock > Source : INTERNAL_OSCILLATOR 

Arduino >Tools > Serial config : ONE_UART_ONE_WIRE_TWO_SPI

Connect GND, VCC, SWC, SWD, Reset to ATMEL-ICE

Arduino > Tools > Programmer : ATMEL-ICE Arduino > Tools > BURN BOOTLOADER

• Now you can upload sketches with USB

Or second option:

From Atmel Studio write special ARMABOT.bin then you can easy upload firmwares drag&drop