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He is from America. The question should be : Where is he from?

He is in the classroom. The question should be: Where is he?

I don't figure out : The sentence constituent of the phrases in these two sentence are the same, but why the questions are so different, why the first question should have the preposition"from" ? So "Where" refers to a preposition phrase or a noun phrase?

1

Where is he from?

could be paraphrased as

Where he comes from? Where was he born?

Note that what we mean here is not "where is he now" but "where was he some time ago?" So we need this 'from' to indicate that we're asking not about the person's present location.

On the other hand, in

Where is he?

we are asking where is the person now, at this moment: it is likely that the asker is not aware that the person is in some room: he may well be on the roof of the school, or at the parking lot talking with a friend. Thus we limit ourselves to the bare form of question, without a preposition.

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