Yes, that’s one way. There’s so many ways.
On most Raspberry Pi operating systems there’s a feature where you can ask it to run your script during a power down but before the power is turned off. You can have that script send serial or set a GPIO pin. Then the Arduino sketch could wait for either the serial data or the GPIO pin and respond by sending a go dark command to the Neopixels.
There’s also a feature that keeps a script running; it starts the script during boot, and stops it during the lead up to power down. If that kind of script was to regularly send serial or toggle a GPIO pin, then the Arduino could wait for the serial data to stop, or the GPIO to stop changing, and respond by sending a go dark command to the Neopixels. That way if the script on the Raspberry Pi fails, the Neopixels will go dark too.
Yet a third way would be to do away with the Arduino and connect the pots and the Neopixels to the Raspberry Pi, but that will require much more work. In particular level shifting the control signal from the 3.3V power domain of the Raspberry Pi to the 5V power domain of the Neopixels.
Hope that helps!