So I did some testing with different configurations of boot loaders and start up code...
Atmel START generated code: 6.5mA
Sparkfun SAMD21 Dev Bootloader: 8.5mA
Adafruit Feather M0 Bootlaoder: 16.9mA
Arduino Zero Bootloader: 17.4mA
To account for LEDs these are the minimum current draw seen over 5 minutes on an Agilent 34461A. It seems like the Sparkfun version of the SAM-BA bootloader is somehow setting up the chip in a more power friendly way than the Arduino version.