These are now supported in modern Arduino chipsets. here's an examples of how to create multiple I2C/SPI peripherals.
https://github.com/adafruit/ArduinoCore-samd/blob/master/variants/grand_central_m4/variant.h#L177

they are auto-generated here:
https://github.com/adafruit/ArduinoCore-samd/blob/master/libraries/SPI/SPI.cpp#L469