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Eventually I figured out that our Vio LDOs had memory characteristics. Charge would remain on the pass transistor gate. Turns out, LDOs need power to *turn themselves off*. So if an LDO crowbars its own input rail, then it doesn't matter if you lower the enable signal.
The whole thing dying meant EN would go low. But that didn't matter. Without Vin, the LDO can't turn off. Powering down the whole Glasgow didn't matter. Power it on again, and current flows through the LDO before Vin can rise enough for it to function, and turn itself off.
The multi-pronged fix for this ended up being adding a large bulk capacitor after the USB current limit IC (whoops, missed that in the datasheet), and adding current limit resistors in series with Vio LDO outputs.
Glasgow revC1/2 can now withstand Vio shorts without not just not locking up, but not glitching at all. The 5V rail briefly dips slightly when you do that, but not enough to disturb the FPGA/FX2 supply rails or trigger the reset monitor.
I can't remember if the final component choice was such that shorting *both* Vio rails *at once* was safe, but if it isn't (which probably also depends on your USB cable/supply), the worst that will happen is the whole thing will reset, and instantly recover with Vio off.
Somewhat relatedly, Glasgow has been tested with I/O pins shorted (in both directions, sourcing 5V straight to ground and sinking straight 5V down to ground) for ~48h with no ill effects. The shifter gets nice and toasty, but survives. It's designed to be unkillable by accident.
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