Fine pitch fab, and low voltages, don't do much for the pins: they still have to deal with the physical reality of huge (relative) chunks of metal being charged to comparable voltages and transmitting electromagnetic waves. A typical SSTL signal might have to deliver 10mA per pin, so the transistors are at least that big. Not necessarily as robust in reverse, especially if reverse bias causes charge injection and further problems (CMOS latchup?), but surely on the same order.
I recall Altera typically warns to avoid peak currents over 10mA or so, and DC over 2mA, in or out of FPGA pins. They're surely small, but they still have to deal with the fact that they are pins. I'll admit FPGAs are probably on the more robust side of nano scale fabs, being that the IO banks often have to operate up to 3.3V, with a variety of configurations (anything from LVTTL to LVDS..), whereas CPU pins might only operate at 1.2 or 1.5V with an SSTL type design.
Tim