Ask Atmel. I didn't write the document.
The maximum current through an I/O pin's protection diode is specified in a bass ackwards way. Basically it can handle any current that doesn't cause the pin's voltage to exceed maximum ratings. Could be tested ... I suspect significantly higher than 1mA (2-3mA??) would still be fine.See 4.9.1 General I/O Pin Protection here.
But isn't the maximum pin voltage just one diode-drop away from the supply voltage? Thereby limiting the current to "none at all" or some complex calculation based on the exact I-V curve of these curiously-unspecified diodes?