Atmel Xmega ADC input voltage range - Can the ADC be damaged by exceeding it's reference voltage, if the input is still less then VCC?
Don't exceed absolute maximum ratings (in fact stay within them as much as you reasonably can). Exceeding Vref isn't a problem providing you don't exceed absolute max ratings. One table is the "don't ever do" table and the other is "don't expect it to function if you do" table.

EDIT - The Vref operational rating of AVcc-0.6V relates more to the DAC outputs on the XMega. DACs share the same voltage reference as the ADCs and because they use the same AVcc power rails, I guess the outputs are restricted to AVcc-0.6V in order to produce non-clipping signals without resorting to extravagant rail-to-rail output amplifiers.