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@unboggling - you seem to have a "bit of an obsession" about the format internal metadata. Personally I don't concern myself with it. As you have mentioned above there are way too many restrictions over what formats support it and to what extent. So rather than relying on it, instead use Calibre the way it is meant to be used - storing it's metadata internally in the database backed up to the opf files. Hence imho copy to library is the "best" way to transfer books between libraries.
The only time the internal metadata should matter is when you make use of something that relies on it - such as some devices. However provided you "properly" transfer to your device either using Save to Disk or Send to Device, then your metadata will get updated for it at that point. And more importantly you can override the metadata to do things like prefixing the metadata title with series etc in the plugboards.
Personally I don't think recommending people use Save to Disk instead of Copy to Library is the right thing. I understand it may be a preference you have but I don't see a valid reason for it when transferring between your own local libraries and there are too many downsides depending on the format.
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