Success at last.

The latest incarnation of the circuit seems to be much better: the signals to/from the Pi are now separated and behave themselves, and the dc-dc converter is definitely off (<1uA current) normally.

The 3 second delay prior to shutting down still isn't working, but maybe that's an OS problem that will eventually get fixed in some later update... For now, I think it's safe to use as a NAS will real data on it!

I've now got an 'ideal diode' module, so will try swapping it for the main Schottky so that the supply voltage doesn't bump up and down so much with load current.