Thanks for posting this, looks interesting, especially with all the pin information and attributes 
A similiar question also popped up in Programm SAMD21 directly and created an example repo GitHub - maxgerhardt/pio-custom-samd21e17a-board: An example on how to define a custom board for the Atmel SAM platform and the Arduino (Adafruit variant) framework for creating a custom Arduino variant for the Adafruit SAMD core.
This also works without
doing this, just using the variant and variants_dir option. Are you sure this is needed?