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The reason is that you may create massive problems for yourself by trying to individual remove and replace indivdual treads and risers. Ordering the stairs pre-fab is the only way to fly....
That said, I suggest using only an oil base stain. I have yet to meet a water based stain I like.
Varathane is but one brand of polyurethane. It's good. I have used it. I'd use it again but don't find it any more or less superior to other brands. Considering the price (near $40 US a gallon here) I usually do use other brands...