because this way it becomes integrated with most of usual file explorers. and i find that more convenient than using a separate program. (in windows) right clicking -> send to -> compressed (zipped) folder and renaming extention to pk3 sounds simplier for me than using w/e standalone program
pk3 = zip, though. I usually just switch file extention to zip when I need to edit a pk3. Unless you are using some non-standard ZIP format it should be alright.
