I think you may be overthinking. Note that 24VAC transformer is always isolated from the mains — the two wires coming out of the transformer, neither of them has galvanic connection to the mains, or the earth ground. So the ‘GND’ on OSPi is just a logic ground, it has no connection whatsoever with the mains or the earth ground. If you are worried that the USB’s ground is earth ground, that’s totally fine, all that this means is it’s going to tie OSPi’s GND to earth ground, but there is nothing wrong about that.
When you have two circuits (such as OSPi and RPi), it’s typical that the ground of both circuits are shared — this is important for all the logic level signals to work. If their grounds are not shared, the voltages would be referring to different reference points, and the two circuits cannot work.
You said “‘GND’ lead from that supply is not actually at ground potential” — I don’t know what you mean by ‘ground potential’ — did you mean logic ground, or earth ground?