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The editor just keeps the parsed OPF as an lxml tree and re-serializes it, so no automatic changes should happen to the package version and so on. That said, the editor, like the rest of calibre has no support for epub 3, so if you plan to work on epub 3, it is best to be careful and turn off automatic metadata update.
The OP's error message actually does not indicate an invalid epub 3, it just indicates that either whatever was used to check the OPF does not understand how XML namespaces work or there is an extra attribute on some tag. Neither condition means that the epub 3 file will not actually work.
As is usual with epub validity checking, finding an "invalid" epub file is more likely to indicate that the tool you are using to check the epubs is pathetic rather than that the epub will actually not work anywhere.
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