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English structure "What do you mean by..."

When 'mean' is used as a verb, sometimes followed by the preposition 'by'. This structure often puzzles me. Compare:

What does 'hermetic' mean?
What do you mean by 'hermetic'?

These two sentence are equivalent. But we may say, 'hermetic' in the second sentence, the questioner might somehow know the meaning, but not sure the meaning in specific context.

Once upon a time, when Confucius paid a visit to Lâo Tan, they talked about benevolence and Righteousness. If you have some background of the Confucianism and Tâoism, you might have known that these two sages held different views of benevolence and righteousness. So, Lâo Tan asked Confucius, 'Let me ask you what you mean by Benevolence and Righteousness.' Here he actually know these words literally, and had different meaning in his own thought. But he wanted to make them clear when Confucius used them.

We have another example,

What do you mean by waking me up at this time of night?

To the person who asks this question, waking him up at night is a fact they both know, and he/she can sense something happened, but he/she wants to know exactly what happened, so he/she uses this 'by' to emphasize his point or focus of the question.
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