First of all, the ePub2 spec says, regarding the META-INF directory:
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This directory contains the files specified below [...] All other files found at the “META-INF/” level MUST be ignored by conformant OCF Reading Systems.
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It goes without saying that "com.apple.ibooks.display-options.xml" is not listed as one of the allowed files, so obviously iBooks is not a "conformant OCF Reading System".
Then it says:
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Any extra files in the ZIP archive (i.e., files within the ZIP archive that are not listed within the package files’ <manifest> element, such as META-INF files or alternate derived renditions of the publication) MUST NOT be used in the processing of the OPS publication.
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which first implies that META-INF files should not be included in the <manifest>, but then says that if it is not manifested, it must not be used for processing. If iBooks is using this file for processing, as it does, it should be manifested, and that implies it should not be in the META-INF directory (where it is not allowed anyway, as we saw above).