No, the authors of the thousands of perfectly working levels and addons released had no idea how to make a pk3 properly...
Packing a pk3 is nothing but creating a pseudo base folder, which is often called a mod folder. That folder plays the role of the base folder in the pk3. Base folder is the root of the pk3, so there are no lower directory structures in a properly packed mod. Thus, there is also no folder called "base" inside a pk3, if you have a look at its inner structures in WinZip, because base is the assumed root.
In that mod folder, create subfolders just like you have under the real base of your game: maps, textures, shaders, effects, models, scripts, etc... You name it. Of course it's only sensible to create those folders that will contain custom files. When you are finished collecting all your custom data in the mod folder, select everything in it (but not the mod folder itself, so in Windows Explorer be inside that folder), and compress it all. Then rename the xxxxx.zip to xxxxx.pk3, and you have a perfect pk3, assuming you made no mistakes.
These also a program called pakscape (or whatever it was) that supposedly can be used to do the same thing. I have never used it, though, so I don't have the slightest idea how it works or looks.
Frozen in the past by ICARUS