I'll be interested to see any outcome of this discussion. The only plugin that I have written to date that persists what could be considered library specific information is the new Goodreads sync plugin. In theory a user could want to specify different sync action custom columns for different libraries which would be a problem. However given that a shelf sync requires all the books to be in the same library it really isn't very likely.
That is not to say that there aren't other plugins I may write in future which may have the same challenge of course.
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