Like you said, a jar is a zip file (not a special type, but just a plain old zip), so either library could be made to work. The reasoning is that the average person, seeing a *.zip extension, tends to unzip it. Since the app server wants it unzipped, a simple rename keeps people from unzipping it simply out of habit. Likewise, *.war file also should remain uncompressed.
java.util.jar basically just adds additional functionality to java.util.zip with very little extra overhead. Let the java.util.jar be a helper in posting, etc... and use it.