Yes, you will find that their are always a few books that fall outside of calibre's standard expectations. In these cases you just have to come up with a way to handle things and use them consistently.
One thing I did was to create a personal "Manual of Style" book which I entered into my Library as a standard book. Making it readily available if I need to refer back to it at a later date. I'll never remember what I did for case X a year or two from now!
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