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Just stick to the specifications. Even if most readers now will allow you to create invalid ePUB's and still work, they are still wrong and there is no guarantee they will still work on other readers.
The ePUB format is already quite slim (contrary to what you claim) and compression makes it even smaller. By tinkering with the opf/ncx you might save 10kb, but probably a lot less. It will take a lot of effort and will gain you almost nothing and possibly generate faulty ePUBs.
The 'why is this needed' is an academical question and should be treated as such. Not for publication of books.
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