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I do not think that Smashwords checks it. I am not 100% sure but I think every time I fixed it was because Apple Rejected it, and not Smashwords.
That being said, I would not discount Apple. They are one of the biggest non-Amazon markets, and even if you are not selling there today that could change. I would suggest you make your EPUB Apple acceptable and not worry about the invisible change you are making to the files.
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