EDIT: @lemming
the difference is the USB VID/PID and the LED pins mapping, see the boards_definition_*.h files for details.
for example: ArduinoCore-samd/bootloaders/zero/board_definitions_arduino_zero.h at master · arduino/ArduinoCore-samd · GitHub
About the difference in size, I don't see any difference in size in the github hosted files:
you can see by yourself that the .bin is 6.5KB as expected.