I were a betting person I’d say they have their own board that sits on the Pi and the ArduSub code runs as a Linux executable on the Pi instead of firmware on the STM32.
I’ve been playing around with the Linux build by hacking together my own rough equivalent of the navigator board’s components. I have a PCA9685 PWM driver, an ADS1015 reading the voltage and current values from the current sense, a BME280 pressure sensor, and a LSM9DS1 IMU. If you have the peripherals connected with the right addresses the companion code will detect a “navigator” and switch modes but I haven’t been confident enough in it yet to try it in the water.
I’m also using a Pi4 because it has more UART, SPI, and I2C interfaces than the earlier Pi devices. The fewer USB-serial adapters the better. I’m considering making my own Pi4 CM carrier that has the correct pin headers and form factor to drop in to the existing enclosure.
I kinda wish more of the roadmap would be shared so I don’t duplicate effort on things already in the works.