OnOff SHIM has a weak ~10Mohm onboard pull-up resistor to prevent the need for a long press. Otherwise without the shutdown pin connected it would be floating and potentially subject to random noise induced shutdowns.
You should be able to change your pin in the device tree overlay to an input with no pull, and allow it to be set up and asserted by the shutdown script only. I’m guessing it being set up as an output is what caused your problems - in retrospect I wasn’t paying as much attention to your overlay as I should have.
I’ve updated the Pinout.xyz documentation to reflect the need for 3.3v which, despite my disagreeing with myself, it actually does require.