To my limited knowledge, they don't do any modification. My point was that there's very little point in pointing out mistakes in files you very well could have done stuff to five years ago before reading it and forgot about doing.
That doesn't seem to be what happened here, but in my opinion, if you're going to point out mistakes you think the publishers have made, you should first make sure the mistakes are actually in the file the publisher/retailer gave you. This is what I wanted to check on, and am now satisfied was indeed the case.
I don't think it was that much of stretch to wonder if something like that might have happened with this file, when Joques was describing how things looked in the kepubified version that was created with a calibre plugin. *shrug*
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