I don't think that calibre making a "copy" really has any relevance though (as you can simply delete it from the import folder so you still only have one copy on your computer).
I also don't see how using "calibre" has makes any difference at all to the discussion of watermarking to be honest. If you put a copy of the book on your computer, that surely counts as one of your x copies you are allowed. Now whether you put it in calibre because you want to read it on that computer, or because you find that the most convenient way to then put it onto your device, who cares - either way you stuck it on your computer so it counts as a copy.
But then I am not a lawyer
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EDIT: Sorry, I should have read your and the previous posts more closely. For some reason I seem to be confusing this thread with another thread I saw at some point, doh. Clearly my view is indeed too simplistic