in classic Chinese, 何由 is the inverse form of 由何, and it should be in the inverse form ,however, you can understand it by understanding 由何.
由 [preposition] 1. from 2.because of 3.by(method, means,way)
so 由何 could mean, from what, because of what, by what. I guess, you would less commonly(Ok, at least I would) say,"By what, did you arrive at this conclusion?", instead, you would say,"how did you arrive at this conclusion?" ;furthermore, when you say "how did you arrive at this conclusion?", you would probably mean "It's impossible to arrive at this conclusion. I don't believe it", depending on the context. This also happens to 何由.
In your examples,I think 何由 means "how could".
By the way, I think this word is not rarely used in classic Chinese, I can give you another example from a poem 《茅屋为秋风所破歌》 by the great poet 杜甫, which was picked into the textbook when I was a student.
长夜沾湿何由彻 How could I bear the bad situation(the house is broken and it rains heavily) in the long night , until the dawn comes.