Steve,
One ATXRaspi should only power 1 Pi at 1 time.
For your scheme I think it should work but you will have to modify the script to issue the cluster shutdown and then power off the control Pi.
There is a time limit from issuing the SHUTDOWN signal (and LED pulsing) until the ATXRaspi will return to normal state, if the BOOTOK signal does not go low - about 1 minute.
ATXRaspi assumes 1 minute is enough for a Pi to shutdown and pull BOOTOK low, for it to then cut power off.
If your control Pi waits a longer time for the cluster to shut off, then ATXRaspi will return to normal and you might have to press the button yet again. If in the meantime your control Pi eventually shuts down, then ATXRaspi will not know what happened and you will have to hold the button for ~6 seconds for it to cut power (forced off).
This is an interesting problem. I imagine there are plenty of clusters out there and people have a need to shutoff the entire cluster in a reasonable amount of time without having to SSH into each one.
What is the size of your cluster? And what would be an average cluster size?