It think that Calibre is correct in including all the metadata that you set in Calibre into the .opf file. I do not see how Calibre can sensibly decide what metadata to include, so should include all it is given. Therefore the culprit is the person who supplied that inappropriate metadata in the first place (Amazon), or you for leaving it set in the Calibre metadata after downloading it? Of course it would also not be an issue if the reading software could handle it being present.
One thing that Calibre could perhaps do is provide a warning if it exceeds some arbitay limit, but what that limit should be I have no idea.
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