I would ask support, if they can tell what exactly happens in this situation and if there's a risk of either device damage or temporary functional failure. I fear, you don't get a satisfying answer.
At days of MultiVolt I/O Interface specification, there has been a comment about possible increased leakage currents when overdriving inputs. As one explanation, leakage currents may have increased above reasonable bounds with newer chip technologies.
The other point is, that since Cyclone III publications are accompanied by permanent "watch your step" directions related to 3.3V operation, as if the authors can't imagine that a designer would be ever able to manage overshoots and keep the maximum voltage ratings. Forbidding input overdrive may be another means to save the chip in this view.
Frank