@Jon-Gordon Regarding the I2C pins and using them with the ATmega MCU, it's possible and you were on the right track.
You first need to set the Omega's I2C pins to act like GPIOs (which you did) with omega2-ctrl gpiomux set i2c gpio.
Then you'll need to set them to act as input GPIOs:
This is crucial since the Omega will then allow these pins to float, giving the MCU an opportunity to become the I2C bus master.
For the SPI pins, yes, GPIOs 15, 16, 17 on the Omega are used to flash the MCU and are connected to the MCU's SPI pins. You can use the same gpioctl dirin command on the Omega to free the MCU's SPI lines.
Just note that your SPI device will probably need to be disconnected if you want to flash the MCU again, and you'll have to rerun the gpioctl dirin commands after you flash the MCU.
Note that GPIOs 15, 16, 17 are just GPIOs and setting them to inputs will not affect communication with the Omega's internal flash storage. That's done with the hardware SPI on GPIOs 7, 8, 9.