Non-literality isn't a get-out-of-your-words-free card. There is a clear difference between saying "you appear to be in error" and "I can't understand how anyone could think that", and the difference is clearly expressed by the literal meanings of those words.

Non-literalness is a get-out-of-your-words-free card when the words are normally used in conversation, by English speakers in general, to mean something non-literal. Yes, if you just invented the non-literal meaning yourself, there are limits to how far from the literal meaning you can be and still expect to be understood, but these limits do not apply when the non-literal meaning is already established usage.

And to explicate "I don't understand etc." with "Of course I do understand how you could think that, it's because you're ignorant or stupid" is not an improvement.

The original quote gives the intended meaning as "I am such a superior moral being that I cannot even imagine the cognitive errors or moral turpitude that could lead someone to..." In other words, the original rationality quote explicitly excludes the possibility of "I understand you believe it because you're ignorant or stupid". It misinterprets the statement as literally claiming that you don't understand in any way whatsoever.

The point is that the quote is a bad rationality quote because it makes a misinterpretation. Whether the statement that it misinterprets is itself a good thing to say is irrelevant to the question of whether it is being misinterpreted.