I think tompe is talking about files created with high compression not being able to be 'unpacked' or otherwise manipulated by his Mobiperl scripts. Since a lot of people (I am one) like to manipulate the metadata after we download a file, any file for distribution should be created using normal compression.
I must admit not really getting the issue anyway - these files are tiny. Hard drive space is about as cheap as it gets, and books are tiny. My Kindle has about 180 MB of free on-board memory and a 2GB SD card, and it holds approx 2200 books.
Given that the files are small, and the fact that many people like to manipulate the metadata for viewing on their ebooks readers, I would imagine that normal compression is optimal. You could always zip the files for storage if it's much of an issue.