So I was experimenting with my shutdown procedure and power-down and power-off are pretty useless in that regard in so much as they don't poweroff and halt the CPU but instead reboot it.
However, I have discovered if I used Linux's magic sysrq interface to send the 'Power off immediately' command. It does just that. The led goes out and the dock is dead until power is reset.
Test it yourself. Just remember that it is immediate power off so no syncing of any kind will happen. You will have to manually sync and unmount disks yourself.
echo "o" >/proc/sysrq-trigger
Still handy to have at the end of a shutdown script though.