Both are the same, but from what I've seen, steam updates undertale better (I bought undertale from the website so just guessing about steam). Also if you ever want to corrupt your files after you've played undertale, steam is the better option there.
probably, since any game you buy on steam should stick with your account id, so as long as you don't use a different account you should be able to re-download undertale for free even with uninstalling then downloading steam again.
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