In the second one it sounds like someone has done something purposely to finish the exam. There's really not much difference between these. "will have" attempts to put the reference point in the future and then look back from there in stating what "will have happened".
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tenjingthe use of 'by' in both sentences is correctYes. There's nothing wrong with the by-phrases.
tenjingthey are similar right?Right. There is practically no difference in meaning between one sentence and the other. People rarely use "will have" in ordinary conversation. It's probably used more in written form