For a better understanding, you can do the following: Decompress fonts.zip and compress it again using your favorite ZIP compressor. Although very simplified, this is the essence of what Precomp does. You'll get a result similar to this one:
As you can see, the recompressed ZIP file clearly isn't the same as the original, although the content is the same. Precomp has to find a way to recompress the ZIP file bit-to-bit identical because it is a lossless algorithm and as there are simply too much possibilites, it often won't be successful.
fonts_original.zip 3767090 bytes
fonts_rezip.zip 3659417 bytes