I don't know why Apple has that restriction. I don't understand most things Apple do. It is not about size, since nowadays they want your covers to be large.
Anyway, there is not much you can do directly to minimize the opf-file. But, there are a lot of files. You could try to merge several html files to minimize the number of files. That has no impact (no real) on the filesize, but has impact on the opf file size.
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