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You could also use a program like TweakePUB. It will leave the ePUB intact and you can edit the OPF in for example notepad. However, be aware that changing the opf can be tricky.
Also, where is the line? Calibre adds a whole lot of metadata for its own good, even its own URI sometimes in the metadata tag. I personally always add the Calibre series tag, but I like to keep it at that.
I don't mind Sigil adding metadata about the version used. I do mind (a little) the metadata with the modification date. I do hope that in the next version also the non-DC metadata show up in the metadata editor though.
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