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My current focus is getting something to work when used with care so I can produce a PROM once in a blue moon.
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That's good for anything you intend to keep in-house and not distribute to the wider world, but (as with software) if you mean to distribute it to a wider audience then it probably has to be more idiot-proof.
Even arranging things so that the programmer power only comes on when the Arduino turns on has a potential flaw - what if you forget to turn on the auxiliary supply before powering on the Arduino? Then, you have strong output drive signals on the control lines of the unpowered programmer interface ICs and those drive signals will probably power the programmer interface ICs through the clamp diodes on the IC inputs, causing unwanted / undefined activity.
I actually quite like your idea of a standalone board into which you place an AVR chip which has been programmed in the usual way in an UNO.
Pros:
-No longer has the size / space limitation imposed by trying to keep it inside the outline of an Arduino shield. You can make it physically bigger.
-Power applied to the programmer PCB applies power to everything simultaneously, power removed from the board removes power from everything.
Cons: Need to own an Arduino UNO just to programme the chip, although the chip can be put straight back in the Arduino and re-used again one you've done your PROM programming job. Could maybe put a programming connector on the programmer PCB to allow the micro to be programmed via AVRDUDE or some such, to avoid the need to own an Arduino.