I think that's the way Zimbra works. A client of mine uses it on an ubuntu box, and even though MySQL, Postfix, JDK and various other packages were already available on the machine, the zimbra installation just unpacked the packaged versions below it's install root.
My guess is, it saves them installation script and setup complexity and they provide "known working versions" possibly with some pre-set configurations that would otherwise interfere with a working installation.