Up to six Serial Communication Interfaces (SERCOM), each configurable
to operate as either:
USART with full-duplex and single-wire half-duplex configuration
I2C up to 3.4 MHz
It is an error in the overview of the SAM D21 features in the datasheet. The SERCOM is half-duplex for I2C. USART can't be configured half-duplex.
You can connect via:
All are available on the Pi's GPIO header and on the Arduino. You will of course need logic level translation for a 5V Arduino.
Using UART is probably simplest for you since that is identical to using the USB - you just use /dev/ttyS0 (or /dev/ttyAMA0 on older Raspberries) instead of /dev/ttyUSB0 or /dev/ttyACM0. Just ...