Go figure... just needed a little more patience and the right search terms. I was able to shut down the NTB0104 by forcing GP21 low on the linux side with the following:
echo 21 > /sys/class/gpio/export
echo "high" > /sys/class/gpio/gpio21/direction
echo 0 > /sys/class/gpio/gpio21/value
echo 21 > /sys/class/gpio/unexport
This allowed my pullups to work perfectly!