The .tgz format is the only one that keeps the message meta data allowing for a full restore of messages to Zimbra...
If you really want it to be .zip you would need to open the Zimlet's files and change this line in emaildownloader.
js:
Code:
url[i++] = "/message.txt?fmt=tgz&id=";
to read
Code:
url[i++] = "/message.txt?fmt=zip&id=";