I’m not sure about the TX2, but on the RPi, there are separate spidev “devices” for each of the SS lines. Even though electrically the “two buses” share 3 of the 4 lines, in the OS (at the SW level) they are treated as completely different buses. On the RPi they are called “spidev0.0” (bus 0 with SS 0) and “spidev0.1” (bus 0 with SS 1).
You would have to modify the BrickPi3 PCB if you wanted to change the SS pin. It’s not just a SW setting. Electrically, the SS is connected to GP7, which is pin 26. If you were to switch the SS pin, you would have to make corresponding changes in the RPi drivers. This is not recommended or supported.
If you can’t figure out how to map the SPI SS signal on the TX2 to pin 26, you could control it as a GPIO. You could set the pin to it’s active state, do the SPI transaction, and then revert the pin to it’s default state. You wouldn’t want to hold it in it’s active state any longer than necessary, but you should be able to do it fast enough. As a last resort, you could even bit-bang the entire SPI communication. It’s only 500kbps, and it should work down to at least 100kbps, so bit-banging should be very doable.